Not being able to mod an omni and keep it an omni, makes sense from a "I need to maintain a standard for tournament level legality" angle, because it would open a whole unmanageable can of worms but "oops, you let the omni smoke out" is complete BS from a technical angle and really has no place in any of the games I run. Really, it feels kindof insulting, to be told that it just magically ruins the omni. It'd be much better to just say "It would be a record keeping nightmare and we don't want to open that can of worms"
At the very least, some minor modification to the base frame shouldn't suddenly fuse all the pods in place, locking them in there or preventing something from being slotted in. The mech should retain modularity like a Mercury has, at the very least. And it's ridiculous to think that all the battle armor hand holds and power ports rot and fall off just because you swapped a medium laser for a TAG or something.
a more reasonable approach, IMO, would be to treat customizing the base frame as a much more difficult version of modifying a standard battlemech. Forbid it in any sort of tournament level play, because that's already forbidden for static battlemechs but if somebody wants to do it in their campaign, treat it as possible but incredibly difficult to do well. If you botch the attempt, give the choice of repairing to standard and aborting, or taking a negative quirk related to the part you were trying to modify. if you barely succeed, you get your mod, but increase the difficulty of further mods. if you get a strong success, you get your mod and can make more. Make the difficulty for mods that effect the available pod space, or impact the structure/speed/heat dissipation or other innate qualities of the mech scale rapidly towards impossibility, but make minor alterations a realistic possibility. Swapping an Avatar's fixed ML for an ER Version? Relatively Easy. Doing something about the fixed Arrow Launchers on the Naga? Super Difficult.