Up until (as a previous poster mentioned) LosTech (Old Star League technology) was rediscovered, what I said was true. All MechWarrior games after the first were set post-clan invasion, which is after the Inner Sphere began to recover methods and technology on the creation of BattleMechs. The Clans never lost that tech, so building mechs wasn't as large an issue for them. ... also, pretty much all of the MechWarrior games so far have been pretty Action/Arcadey. It's nescessary to have a multitude of enemies, so the limitations of the fictional universe weren't applied nearly as strictly.
Regarding adaptation, I think you're partially correct, within the confines of the fictional universe. Yes, weapons can be adapted to fit mechs that weren't designed for them, but I'd guess it's extremely unlikely that you could do it effectively in the field. It'd be like taking an afternoon to put a 600hp rotary engine in a Corolla. Also, the weapons may not have been so compartmentalized back in 3015. Sure, you could probably weld on a weapon to a part of the Chassis, but did you plan for the added weight in that area? Did you make sure that enough power was routed there? Do you have localized heatsinks ready to dissipate the heat involved with firing that weapon?
This game seems to be based upon the defense of a fairly backwater planet from a Kurita invasion. Based on that subject, I think it's unlikely that there would be too much customization of weapons possible, if it sticks true(er) to the fictional universe.