Yes it will, the systems are balanced differently in this respect. BRP has a 1/5 chance special success for an impale, which does extra damage, and a 1/20 chance crit that does maximum damage and ignores all armour. MRQ2 has a 1/10 chance crit that, if the opposition doesn't parry, gets you two manoeuvres, from which you can choose Maximize Damage and Ignore Armour, or Choose Location and Max Damage, or Impale and Ignore Armour, or any of a variety of other combinations. But the "double maximum ignoring armour" can't happen in MRQ2, and "ignore armour" is much less common in BRP.
So, if you want to adopt part of one system and part of another, you will have to consider the balancing factors.
Also, armour levels are slightly lower in MRQ2, weapon damage... not sure if that is different, MRQ2 has higher locational hit points but no general hit points, all these factors affect game balance, and (in theory) are designed to be balanced relative to each other.