The percentage difference is the bonus BV the smaller force gets for improving skills only. No extra units, just better pilots.
Yeah, see, this is what I was referring to in my post. The rules for the FSM don't actually say this. And this is where people get all cranky about FSM 'cause they go to a tournament with a 4 mech 5000 BV force, and when their opponent shows up with a 1 mech 5000 BV force, someone tells them they have to give all their mechs 7/8 pilots or whatever.
Except the rules as they were written don't actually say this is what you are supposed to do with FSM.
The rules for FSM are remarkably vague in regards to how you apply it in a given situation. And I suspect that at some point, some judge somewhere at some tournament decided that this (i.e. make someone take pilot adjustments) on the fly, and it stuck.
Using the BV rules as written (as vaguely as they are) indicates only that (using the obvious, simple example) with a 4 unit force vs a 5 unit force, the 5 unit force is penalized by 5% or the 4 unit force gets a 5% bonus (same difference). Which means that given 4000 BV (which is just a nice number to work with for example) force, the smaller force actually gets 4200 BV to spend ('cause the bigger force is actually spending 4200 BV for 4000 BV worth of stuff).
If you are setting up a game ahead of time, you can work this out, and it works fine; i.e. Dave and I are playing a game on Saturday, and we decide that it will be a 4 mech IS lance vs a 5 mech Clan star. We want to use BV and FSM, so we figure out that if we start at 8000 BV, my 4 mech IS lance will get to spend 8400 BV and his 5 mech Clan star will get 8000 BV to spend.
If you just showing up to a game with some number of units for X BV, and then trying to use FSM to balance things out after the fact, you run into all sorts of troubles, and the only thing viable to do is to adjust pilot skills, really. Or possibly, if there is a victory condition rule based on BV, you can award the smaller side a VP bonus based on the FSM, but then, I've never actually seen a BV based victory condition.