I've seen both screws, they both bottom out. The stoptech brakelines for the 2nd gen FX are the same for both the FX35 and the FX50. Part numbers on their site confirm this. So either case, if you use stock banjo bolts or the stoptech ones, they were designed primarily for the FX35 non-sport non-akebono calipers. So having akebono calipers, you'll be using a banjo bolt setup.
I'm not sure its worth upgrading to stoptech lines if you have the FX35 with the sport package or the FX50S. There's enough hardlines in the brakeslines as it is.