I'm sure omnis start to look like a logistical pain in the arse if you're trying to produce enough omni-pods to have every single one of your airframes have access to every single omni-configuration at all times.
I'm not sure why you would even try to do that. There's not going to be a situation where your entire Great House military needs all of their Omni-VTOLs converted to scouts now. You don't need to have a 1-to-1 chopper-to-recon kit ratio any more than you need to have a 1-to-1
For demonstration's sake, let's make a theoretical VTOL battalion out of a Seeker Dropship. Someone decides it needs 4 different VTOL types to perform its duties, for whatever reason:
10 ton Sprint Scout Helicopter (Laser) -> Recon
10 ton Ripper Infantry Transport (Standard) -> Light Slick/Snake
25 ton Cavalry Attack Helicopter (Infantry) -> Heavy Slick/Snake
30 ton Cobra Transport VTOL -> Cargo & Logistical Support VTOL
So for our Seeker Dropship with 40 light vehicle bays, for the sake of simplicity we'll take an even split: 10 of each. (We probably wouldn't actually do that so evenly, but it's just for example)
Each of these airframes presumably fulfill a specific niche that, without them, the task force would perform much more poorly. At least, presumably that's the case: If one of the vehicles or roles turned out to be not all that important after all, why bother bringing it in the first place? So you don't want to run out of such vehicles in the field, as that would presumably cripple your performance, so we're going to want to stow additional VTOLs in reserve. Let's say we decide to store a decent chunk of VTOLs in the cargo for our reserves, 5 airframes each, 20 airframes total: 375 tons worth of VTOLs alone. Only 116 tons are left on the Dropship for other stuff like consumables and spare parts.
Alternatively, I may be able to effectively replicate the lighter end roles into one 11-ton SFE Omni-VTOL with 3-4 tons of pod space and 2 variants, and I could replicate the bigger two into one 24-ton SFE Omni-VTOL with 8-9 tons of pod space and 2 variants, with no real loss in tactical effectiveness.
The alternative Battalion now has 20 light Omnis (10 in a scout configuration, 10 in a slick/snake) and 20 heavy Omnis (10 in a slick/snake configuration, 10 as logistics) in the vehicle bays, and 10/10 "naked" frames in reserve + 5 omni kits for each role, taking up 350 tons and leaving 141 tons to spare, more than the non-omni force.
Currently, the alternative Battalion is actually quite similar to the Standard Vehicle version, and would perform quite similarly on the tactical level. However, it already has a large advantage at the strategic level, as repairs, replacements, and rearming (and overall combat readiness) is much quicker than the conventional force. The price for this is approximately 25% extra up front for the VTOL component of the force. Considering the cost of the Seeker dropship and its parent Jumpship or Warship, that price hike is just a drop in the bucket.
However, the Omni's reserves are actually over-stocked with airframes. Originally we were operating on the assumption of "one-bird one-frame" and stocked the reserves accordingly. What's the probability that we lose both 5 recon birds and 5 light slicks? What about losing and needing both 5 combat birds and transport birds? Depending on the scenario, our recon birds may suffer or less from attrition than the Light Slicks. Since both are using the same frame, we can often get away with reducing the amount of frames we have in reserves while having the same number of pod kits. Say, reduce both the light and heavy VTOL reserves by 2 frames, so 8 light reserve frames are sharing between 5 recon packages and 5 slick packages, and 8 heavy frames share between 5 transport packages and 5 snake/slick packages. This saves about 50 extra tons, some more money, and you'll perform the same as a unit with slightly more reserve frames unless you're in the extremely unlikely scenario of requiring both 4-5 of Role A and 5 of role B from reserves, for the same frame, at the same time. (If you require more than 5 frames at the same time, both the Omni battalion and the Standard battalion are up a creek).
Alternatively, you could go the other way. Do you expect in advance from experience that the heavy VTOL will likely take more casualties in the Slick/Snake role than in the Transport role? The conventional force would have to allocate the full weight of the VTOLs to provide reserve capacity. It often suffices to simply allocate a few more omni-pod kits for the existing Omni Fleet, which is a far less weight and cost intensive way to get the reserve capacity needed. Adding 2 more 8-9 ton heavy Slick/Snake kits is much easier than adding 2 more entire frames, and works just as fine as long as both the Transport and Slick/Snake reserves do not get maximally stressed out at the same time.
Or perhaps you take out your VTOL battalion and- oops, it turns out having a VTOL that's capable of long-range harassing fire is pretty vital! If your force is a standard force, you have to figure out how you want to reorganize your battalion to fit long-ranged firepower, either develop a new design or import an existing one (heavy and more expensive approach), or just ship the weapons and refit an existing one (almost certainly going to be maintenance level or worse, so time-consuming and error-prone). If it's an Omni-VTOL, put some PPCs or ERLLs in a pod, ship the pods, plop the pod on the Heavy chassis, and enjoy. All the pod kits you need for the Omni Battalion's conversion can likely be carried by only 1 or 2 Small Craft (K-1 Dropshuttles) and the conversion can be done in a trivial amount of time, which is much better than the options that the Standard battalion has available.
Or maybe your faction's supply lines have started producing more advanced weapons and equipment. Now that we're producing a glut of IS ER Medium Lasers, so we can upgrade our regular Mediums to the new standard. It's not terribly difficult for a standard vehicle, but omni VTOLs can do the swap faster nonetheless. A few years later, our faction is now producing much more Battle Armor, and they want to refit the Battalions with IS Standards instead of Jump Infantry. Well, our infantry bays are too small for the full squad, so we'll either have to develop, ship and deploy yet another specialist design specifically for BA or our standard VTOL battalion is going to be unavailable as they perform the maintenance-grade (or worse) upgrade on our existing slicks. Omnis? Ship a few new pod kits in a Dropshuttle or 2, and plop them in. We're ready to roll out.
Not that it pertains to war, but the ability to convert a portion of your VTOL fleet during peace-time to respond to disasters in under an hour is handy. Throw a few cheap kits in a garrison and your helicopters can convert for aerial firefighting, post-disaster SAR, or MEDEVAC in under an hour, as the need presents itself. There'll presumably also be dedicated civillian choppers for that, but as we know local governments are always perfectly prepared for any such contigency... Well, maybe not.
Or there's other uses. An omni-VTOL can be converted to assist with infrastructure projects with little hassle, and could supplement or even replace dedicated construction VTOLs. There's usually some government project that needs help erecting, some power lines or transmission towers needing built or replaced, or crops needing dusted, high-speed hovercraft pursuits being monitored (though if you're feeling less than charitable I suppose you could also omni-mount a laser for "enforcement"). Unless the typical service life of your VTOLs is "Build it->Deploy it->Lose it," (in which case the only your VTOLs are helping is your MIC and your military opponents,) the omni-VTOL can (and should) easily pay off its initial premium simply by contributing to the nation's economy during times of (relative) peace. So much for the expense argument.
So that's my excessively wordy essay in defense of omni-VTOLs.