The ejector will protrude slightly in the fully retracted position, you can push in it to lock it in the retracted position, it would be better to remove the ejector for fitting, but not required. If there's a slight gap at the very top of the barrel, it's not unusual, a lot depends on how flat and true the barrel face is, I always file it flat before fitting as long as a sized case is slightly recessed, if not, you're kinda stuck working with it the way it is, if you file it flat, you'll end up with negative headspace, correctable on a rimless round by modifying the die to push the shoulder back more, but not much you can do on a rimmed round short of running a reamer into it to correct it.
Tim