Let's get something perfectly clear here: Fuel is a negligible cost, it's not a scarcity item, it's not even a particularly complex item, this isn't the 1970's. anywhere you've got enough infrastructure to HAVE a garrison, is going to have plentiful fuel. (hence the popularity of ICE vehicles).
Second "Easy to maintain quirk" is relative to other units of equal tech. a fusion engine that's 'easy to maintain' is still going to be more expensive to upkeep than a fuel cell or ICE engine of the same rating. In this case, "easy to maintain" is relative to another Omni-VTOL with a Chin Turret.
Third, "Changing roles on the fly" requires the pods-which are a logistical cost-when not in use, you have to have them on hand, and while they're not in use, they still require maintenance and upkeep, still require warehouse space, still require shipping space. Further, it requires being able to move a repair site rapidly so that your 'change' can happen quickly enough to justify the expense, which requires more specialized assets to move your unused pods around the battlefield or close to it, which also requires guarding forces for the technical crew, ordnance, equipment, convoy guards, convoy vehicles...and this is above-and-beyond standard ammo and fuel convoys too, since the cargo isn't 'immediate use'. Plus administrative costs tracking all those pods and getting the right ones to the right positions.
fourth, since you can 'change roles' by changing equipment, you still have to either send your techs through constant refresher training to keep up, or have a larger ground crew organization to keep those pods in shape to be used. additionally, your pilots have to go through more varied, less focused, training to be able to USE those additional features. These all drive your costs upward as you lose the ability to focus training-your crews, if they're the same size, aren't going to be as well trained and efficient, and damage/losses in training roles are going to be higher. Alternately, to have the same efficiency in operation will require pilots to have hundreds (if not more) additional hours requalifying with each configuration you are using, and a signifcant additional manpower cost to have enough repair trained personnel to upkeep the additional pods.
not including additional base-guards, larger perimeters, (to contain the additional materials), additional structures (to contain the added items), with different individual needs (because a cargo box differs remarkably from a PPC, which differs from missile ammunition which differs from electronics).
all of that, in turn, requires shipping tonnage to move.
but there's more!! because procurement costs, also, go through the roof. Omni-anything costs more on the production end. (Hence the abandonment of Omnimech and omnivehicle efforts by 3067 and conversion of so many of those projects to fixed configuration versions). You pay more at the factory door, and then you pay more for what you're shipping to the garrison, and then you pay more to keep it in garrison, or you pay astronomically more shipping between garrison locations.
Your administrative, materiel and protection costs go up for the same role significantly the more configurations you're willing to deploy per chassis, and you've basically sacrificed core abilities in comparison with older, more effective designs for a chassis that doesn't do anything particularly well, besides renumerate the contractors and strain your personnel and logistical budget.
1.Fuel costs are in no way negligible. According to the Strat Ops fuel table (pg.179) the typical cost for a ton of Petrochemical is 1,000 C-Bills (1.2k for natural gas, 15k for Hydrogen, and 1.5k for alcohol fuels). By Techmanual errata, a fuel consuming engine (ICE, Fuel Cell) is assumed to have 10% of its engine mass as fuel, and by the support vehicle rules an ICE has 100km range per every 1% of the engine's weight as fuel, giving 1,000 km ranges for ICE vehicles.
A Karnov with its 15 ton ICE engine would have 1.5 tons fuel for a 1,000 km range (A bit better than a Eurocopter Tiger). A full tank of gas for the Karnov will then cost 1,500 C-Bills, more than a ton of regular AC/2 or Machine gun ammo costs, and being a standard cargo helicopter in the Battletech Universe where nothing ever seems to become obsolete it's going to be operational for decades if not
centuries, operating again and again racking up thousands of flight hours. Not only will that fuel cost add up, a fusion alternative like the Cobra VTOL (or the Wyvern) can easily become the cheaper option in the long run.
That's just for civillian or garrison duties. In long-term offensive operations, the accompanying Dropship, Jumpship, or Warship will need to carry spare fuel in their limited cargo space, which could otherwise be used to store extra weapons, ammunition, or spare equipment, with the exception of short raids.
2.Fusion engines and Fuel Cells on Combat Vehicles are both Tech Rating D, so their levels of complexity are equivalent as far as Strat Ops's repair rules are concerned. Upkeep would then be similar, except the Fusion doesn't need any significant fuel to speak of while the Fuel cell does, so it's inferior with respect to upkeep. A SFE attached to a unit with the Easy-to-maintain is equivalent to an ICE engine (rating C for combat vehicles) as far as maintenance checks are concerned. It is relative to units of equal tech but a Fuel Cell engine is comparable to a Fusion engine as far as BT is concerned, so claiming its upkeep is lower is just wrong.
3.There is not a single universe where standardization results in a logistical penalty.
In terms of VTOLs alone, the Fed Suns have available to them, in various eras, are variants of the Ferret, Cavalry, Martens, Strixs, Hawk Moths & Hawk Moth IIs, Mantis, Nightshades, Peregrines, Warriors, Yashas, Yellow Jackets, Karnovs, and Cobras.
Many of these would be operational in numerous AFFS units throughout their territories at the same time. Most of their engines are incompatible, their armor types often differ, their Comms system & Targeting systems are usually different, rotor arrangements differ, and even between different models of the same nominal chassis may be almost entirely different (The H-7 Warrior vs H-8, for instance, effectively has a different chassis (21 tons vs 20 tons, 3 IS vs 2 IS), different armor type, different engine type and engine rating). So if you're part of high command in charge of procurement, your dozen or so Helicopter models and their variants has you keeping track of a half dozen or so T&T & Comms systems, rotor systems, potentially a half dozen different armor types, and easily a dozen or so different engines across your VTOL fleet alone.
Replacing many of the heavier VTOLs with a "standardized" helicopter cuts down the number of frames, engines, rotors, and such substantially. Replacing your standards with a few (2 or 3) Omni-VTOL designs of various weight classes to replace all but perhaps the most specialist designs would cut the frames, engines, rotors you have to keep track of for your VTOL fleet. They generally won't do any particular job quite as good as the dedicated specialist but if it's good enough then it's hard to argue against the logistical benefits of condensing your 20 different VTOL frames down to 2 or 3.
In addition to being common sense, such logistical advantages of Omnis are also hashed out in fluff as that was among the chief advantage of the Clans were stated to have. Standard battlemechs and vehicles also need to have replacement weapons and parts on hand because even in the future nothing works 100% of the time, so infastructure exists for such equipment, the only difference being these new ones are in pods.
Literally the only situation where an omni-VTOL would cause higher logistical strain is if you replaced
only 1 non-omni VTOL model that does
*all* the jobs and gruntwork with an omni-VTOL with several variants. However, such a non-omni VTOL capable of doing every single job required by any house's military doctrine does not exist, so realistically there's going to be (and is) several, if not several dozen, models and variant floating around for the quartermasters to manage across your armed services unless you either simplify your doctrine somehow such that you need a mere handful of different standard VTOL models or replace them with an Omni to continue using your current doctrine.
4.No such penalty actually exists for techs or vehicle crews having to swap to a new vehicle or variant, omni or otherwise. There is no penalty for a pilot that moves from a standard 3025 Battlemech to a field refit model. There is no penalty for training an omni vehicle pilot compared to a standard vehicle. There is no such penalty for the astech crews that have to operate on the things either: In fact, the maintenance effects are exclusively positive by reducing rearming/replacement times. It's a weapon system. It's not like a LAM where the pilot has to figure out both how to fly in Aero form, glide around in AirMech form, and walk around in Battlemech form, it's just a weapon system, and quite frankly if your pilot cannot figure out how to fire a laser versus an autocannon or a gauss rifle, the pilot should have washed out in Basic.
Specialized training would only be really necessary in specialized roles like reconnaisance and special operations roles. The various "front-line" VTOL configurations would be operable by any regular VTOL pilot.