I have never found it an issue to have the studs out high - if that is what a set up needs, then that is what it needs. I don't hear a difference in sound and I don't mind the esthetics. Not getting the bridge low enough and then having to snug it against the body plus file the slots deeper is certainly more worrisome. The overall tendency of Epi and Gibson has been in the last two decades to structure the basses in a way, i.e. angle and set the neck high enough und use lower saddles, that the the three point always has room to go lower if need be. That wasn't so with many basses in the seventies where the range was more limited. I have TBirds, a Flying V, two Rippers and the Les Paul Sig where in my opinion the bridge is not really well-aligned to the (low) height of the neck and where as a consequence you need to screw the bridge snugly to the body.
