i think one of the ways they tried justifying intercorporate skirmishes in the mutant chonicles fluff was by emphasizing how scattered the corporations were throughout the solar system. that is, the corporations on the "small scale" could engage in conflicts in one area without it being the "whole" corporation going off to war, while the corporations as a whole even continued engaging in trade at the same time. with mishima, for example, you have the three lord heirs doing their own things on their home turfs (mercury, venus, or mars), duking it out with other corporations indirectly through only one of their vassals, who might engage in border skirmishes with capitol on mars, for example, or try to take an isolated research facility from cybertronic, etc.
in the capitol fow, for example, it also casually mentions how the government can engage in small to medium sized battles at a regional level, without really involving capitol as a whole. when it gets bigger, though, then its taken to the top levels of the capitol political structure.
but then there are also scenarios which are not supposed to work at all, such as the brotherhood fighting anyone other than cybertronic or the dark legion. you would then have to come up with (if you cared) a good fluff excuse, such as it turns out commander so-and-so was a heretic of semai who brainwashed all the soldiers under his command or something.
finally, theres the fact that wz is set in the start of the second corporate wars... so no excuses for corporations to attack each other if youre including that as part of your fluff background.