Sounds like you should definitely go with 50mm spacing then. As for covers, here's a quote from Tim:
"Covers effect the tone slightly, they roll in the highs and warm up the bass, kind of instant vintage vibe so players who remove a cover often comment on how much more 'air' or presence they can hear... I can compensate in the wind for this."
So for a bit more presence/brightness, go open. Personally I like covers, but just for the look and the fact they protect the pickups, I'm not bothered about the effect on the tone one way or the other - BKPs never seem to lack presence anyway. It may be shallow, but I'd say go for whatever you think'll look best. :D