Yes, I think it’s better to leave a small gap to be able to balance better. The problem is the difference from door frame to door frame.
It sounds like the REV A jig leaves more space to balance so might be better for now. Let’s leave it how it was and not use the REV B hinge jig.
I don’t know why you need to hit the locator with a rubber hammer- you shouldn’t need to do this. If the hinge is off centre- adjust the glue jig hinge to glass position to fix.