The omnismoke ruling does stem from a real world rationalization. A half-remembered and possibly mistaken one perhaps, but a real world rationalization nonetheless. It does not exist merely "because the rules say so" (and indeed, no published rule actually supports it). Discussing the rationalization behind the rule is relevant and useful in the context of a practical question posed by the OP - please do not ever come into a thread like this and advise people to turn their brains off.
If the rest of what you said is an argument you really want to make, I am willing to address it point by point, but as it's not topical to this discussion I ask you open a new thread for it.
I had thought the rationalization was balance. This rule, after all, only affects campaigns. You can create any custom 'mech you wish, no matter how ridiculous (I recall the existance of a "Quad Urbie LAM" kitbash for example). The only time the benefits of an Omnimech comes up is when you're repairing 'mechs between linked games and need to track the time and what you have available in inventory for repairs and switching loadouts.
I may be mistaken, but from what I remember, to mount a weapon on an Omnimech requires it to be in an 'Omnipod' which is proprietary to the weapon. If you salvage a LRM10 and have to decide if it goes on your Avatar or your Atlas will depend on whether the LRM10 came in an Omnipod. If it did, you can spend half an hour installing it into your Avatar or remove it from the pod and spend a few hours to put it into your Atlas and risk penalties to your gunnery or piloting if your tech screws the job up. Clearly the Omni has a benefit here.
If it doesn't have an Omnipod is where things get problematic. As far as I know, you can't take the Omnipod off a Machinegun and slap it onto the LRM10, which means you're going to have to hard mount the LRM10 onto the Avatar as fixed equipment. The time is the exact same as it is to do it on the Atlas, with the same risks of penalties. If there is no drawback to doing this to the Avatar, then as I think TPTB said, what's the point of non-Omnis?
I'm not sure if the ruling was really well thought out though. Let's say I don't
have an Atlas- just the Avatar. Let's further say that the Avatar took significant damage- it lost it's right torso in the last deployment, and we're doing a repair job. We fixed the XL engine, repaired the torso, managed to save the Artemis IV (with Omnipod!) and re-attached the severed arm. Regrettably, the LRM10 died and has to be replaced- no Omnipod for the LRM10 we have on hand though.
Okay.
Fine. We let the 'smoke out' or whatever and we'll hard mount the LRM10 as fixed equipment, sans pod, with the associated penalties and this Avatar is now
permanently a standard Battlemech. Opfor is inbound and it's better to have a fully functional Battlemech than a mostly intact Omnimech right?
Here's one issue I have: Battlemechs can't take Omnipods. The other LRM10, the LBx10, the machine guns and medium lasers and the Artemis IVs
no longer work. The tech will have to pop them out of the Avatar, remove them from the Omnipods and then
put them as fixed equipment.
Why?
Especially, as in the Avatar's fluff comes across as the developers didn't have to do all that during testing. It says that the medium lasers were faulty during testing so they "hardwired" them into the chasis and then switching them back into Omnipods got lost in the paperwork after they had the issue with medium lasers sorted out. It doesn't sound like the prototype reverted to a standard Battlemech, permanently, and they had to redesign the whole prototype around the medium lasers being fixed equipment. To me, anyway, it sounds like the medium lasers didn't work so they hardwired them, then had a working prototype (with the 'smoke' still in it) and swapped configs just fine...and then sent the specs off for production before realizing they forgot to say "switch the medium lasers back to omnipods".
In a world where refits exist to upgrade 3025 'mechs with endosteel and XL engines were meant to be done in fully equipped 'mech bays... any re calibrations that the Avatar designers did should be possible.
In my opinion anyway.
Furthermore, while I understand the intent that Omni technology is a "flexible weapon" but also "fragile", this technology lets me put whatever I want onto that Avatar chassis so long as there's room. Not only do we have some really big, significant changes between canon configurations (Mad Dog Prime to Mad Dog C for example) but they'll take
anything so long as its an Omni pod. That LRM10 not in an omnipod? Fine, let's cram some Omnijumpjets in there instead- who cares if they're all in one torso and we did it in an hour? That Avatar will fly
anyway. This doesn't even touch upon the utter trauma Omnimechs can sustain and continue to function: Entire torsos can be removed by all sorts of abusive weapon fire, limbs can be forcibly removed in combat, blunt force impact of charging hovertanks, flooding of entire compartments with saltwater, explosive decompression in vaccums etc. etc.
And the Omnimech's omni components will keep working- even if the mechwarrior isn't. Salvage an Omnimech that's missing its right half, and don't have a replacement leg? No problem, just pop whatever's left out and pop in an Omnipod Gauss Rifle and use it as an immobile turret to rain supersonic watermelons down upon the enemy from the bay door of your dropship.
But hardwiring an LRM10 in place of an Omnipod LRM10 renders the Omnitechnology...useless? For good, because it's not smart enough to accommodate for the reduction in pod space? Replacing FF armour on your left arm with some standard armour because your back is against the wall will shut down your entire weapon load out and forever mean it can't take Omnipods because...why, exactly?
Personally, even without this ruling, I still wouldn't hardwire a LRM10 into the Avatar if I had other Omnipod weapons available because that's the whole point of having some Omnimechs- and the freed up time can be better spent working on my non-Omnimechs.
The logistical nightmare and scarcity of purchasing and salvaging Omnipod ammo bins and components is more than enough of a drawback to keep Battlemechs relevant for me, personally. Why limit yourself to one or the other when you can have both?
EDIT: Just to clarify as I realize I probably contradict myself by saying I can understand "what's the point of standard 'mechs?" only to conclude that the scarcity and logistics is enough to justify keeping regular Battlemechs around at the end. In the 'future' (say 3250 or whatever), if
everything is Omni technology then whatever you salvage can be simply popped right onto your 'mechs after the battle. Omnis do render standard 'mechs obsolete in that sense- however, we have so much handwaved away already in Battletech, saying that the new technology in 3250 continues to favor standard Battlemechs over Omnimechs isn't a big obstacle in my mind. I'm sure plenty of 'plausible' reasons could be used.