I would contact Bare Knuckle and ask them some questions. I want to say this doesn't sound quite right and yet I also know how much construction impacts tone.
N00b Qu3sti0n
Have you checked all your solder joints? Are there any cold solder joints?
If the wiring is 100% in place you really have two options:
1) Something isn't quite right with the pickup. This is unlikely, but it happens.
2) The pickup simply is not taking to the guitar.
Try swapping the A-Bombs between the two guitars and this will address both these issues.
My Rebel Yell bridge pickup was bright and almost overly thin sounding in my Les Paul Standard. When I put the Rebel Yell in my Godin LG, the pickup became alive. It was phatter, warmer, raunchier, and more aggressive, and it still had that wonderful harmonic spread and wide pick attack. It made the guitar crazy good.
The A-Bomb in my LP standard has this crazy throaty roar and it sounds big, open, and huge. I suspect it would sound mammoth in the Godin LG.
The possibility exists that you may have to try something else in the strat if heft, beef, aggression, and roar is what you're after. Juggernaut, or A-Pig hahahaha.