When you were modding the purchase files, did you find where the default/starting mechs and mechwarriors are defined?
Whenever you play the original campaign you start with Beast, Hawk, Hunter and Lynx, along with two Commandos and a Firestarter.
What I've found is that these mechwarriors and vehicles don't look at the related PMWxxxxx.FIT or PMxxxxxx.FIT.
I modified the weapons on the commando but it only affects mechs I buy or fight, not the starting two.
Likewise I changed the colour of some mechwarriors but Beast, Hawk, Hunter and Lynx aren't affected, only those I buy or am gifted (like Falcon and Firestorm).
I'm worried this might be in the .exe but maybe you know better.
From what I remember of the player created campaigns, the ones set on Port Arthur use Beast, Hawk, Hunter and Lynx, but the ones set on Cermark do not use the expansion starter mechs/mechwarriors. I definitely remember one with Mystique and Baron.