My guess is that building a mech, and particularly an Omnimech, is more difficult than the simple calculations we use when designing one in the game.
It's one thing to take a Warhammer, and write on a piece of paper "remove machine guns and ammo, add 1 ton armor and 1 heat sink", and then add a few points of armor to different locations. It's another thing entirely for some techs in-universe to go into the chassis, take out the machine gun housings, remove the ammo feed, find a place to wire in another heat sink, and then balance the additional armor in a way that lets the mech move about freely and provides even protection across entire locations.
One is easy. One is probably pretty hard.
My recollection of the Avatar is that the two hard-wired medium lasers were a result of a glitch they couldn't get fixed. And while there are no in-game rules for building a mech that doesn't work right, even though you followed the construction rules, "real life" in the game is different. Negative quirks can simulate that, but the basic design rules don't account for it. The Bushwhacker is another example of something that would have been perfectly book legal, but doesn't work for some reason.
Swapping out fixed equipment on an Omni seems like something that could cause a lot of problems, but doesn't necessarily always do so. The Avatar example, I wouldn't have a problem with somebody swapping out medium lasers for ER mediums. It's the same weight, the same number of criticals, even the same basic type of weapon. But changing from regular internal structure to endo steel, you've got to rebuild the entire mech. Yanking out an ECM suite and C3 for an anti-missile system and extra heat sinks, that requires changing the mech's targeting systems, rerouting coolant lines to a place they didn't go before, that kind of thing.
I can see how doing that might interfere with the carefully-designed pod system. Like making three or four random moves on a Rubik's cube.
