Omnis are fairly stupid premise-wise, because improving modularity should make something cheaper to work with, not more expensive. I get that it's supposed to be a balancing thing, but they should've just made the better components themselves more expensive rather than try to have a bizarre tax on standardized construction. That thing that made the industrial revolution possible and propelled humanity into our joyous future.
The in-universe explanation is that everybody simply
gave up on standardizing ammo, data, coolant and power ports because there are roughly a
billion different manufacturers and models for everything, across the entire Inner Sphere. Worse, with salvage being what it is two Defiance B3M Medium Lasers may be technically from the same
manufacturer and model, but since one was manufactured 150 years ago the design has drifted since. Even in the Clan Homeworlds, things built by one Clan don't necessarily follow the same patterns as the other clans. The solution, instead of getting everybody to shape the fuck up and
standardize on a single pattern, was to create OmniPods.
OmniPods are finely engineered shells that fit around the module in order to bring it up to the correct dimensions and line up all the ports so they fit in the standardized pod bays inside OmniMechs. They don't take up any additional crit slots in the 'Mech's paperdoll because the
modules themselves don't take up all the space the game's abstraction says they do. A Small Laser takes up the exact same 1 crit slot as a Medium Laser, but the weapons themselves are different in size. Since all the internals of a 'Mech are irregular in shape, designing a BattleMech is basically a huge game of Tetris, trying to optimize how everything fits around everything else and routing ammo, power, data and coolant lines. OmniPods take up slightly more space (not enough to actually count as crit space), but make it
much easier to just slot things in and out by vastly simplifying the routing.
In computer terms, think of them as the equivalent to caddies that let you affix 2.5" SSDs to 3.5" HDD bays. Two PPCs of different models may look
completely different before being installed into OmniPods, but after they are installed, anything behind the barrel (the stuff that's hidden inside the 'Mech itself) will look the same: regular cuboids with attachment points and ports on the same locations. That's why you can't install a piece of equipment that was mounted into an OmniPod into a non-OmniMech. You have to rip out the shell first, because the OmniPod takes up too much space in the cramped guts of a normally-designed 'Mech.
That's why OmniMechs and gear mounted in OmniPods are more expensive. They're a solution to the inability of the people in the setting to agree to any standards in manufacture. The pods don't so much standardize parts as they serve as a kind of "emulator" (or a compatibility layer, I guess?) between the parts and the 'Mech, and all that equipment has a cost. The OmniMech itself needs a much better gyro and battle computer in order to accept the plug-and-play nature of OmniPods (this is the setting that has targeting computers weighing multiple
tons). And finally, the pod bays also have to be built to tight standards and tolerances in order to take in the pods.