Couple of useless points here. First, I'm not too impressed with the Dremel press. It's not a consistent pinpoint precision machine, at least mine isn't. Half of it is plastic. There's an obvious deviation from straight in the drill bit stroke as the lever is pulled. So, I've learned to find where the deviation is at minimum during the stroke and go that route. Also, there are several brass adjusting screws, that can easily be missed, that should be adjusted to gain the straightest stroke path as possible. There are at least three of them, I think.
Moreover, I've learned to sand each side of the jog slightly to help it lay perfectly flat as possible.
Next, was to stop using the Dremel station altogether, and use a decent drill press.
OP, if I were you, I'd sand the top of the housing, as you said you would. The height of the housing *may have something to do with it being a Gen 5 housing. A trick to gain more cruciform engagement was to switch from a Gen 3 housing to a Gen 4/5, so maybe housings after Gen 3 sit a little more proud, thus giving you some issues.
I would, however, like to hear more about why slides can get hung up and not return to battery more smoothly when the trigger is held to the rear. As far as I suspect, it has something to do with the verticle extension on the safety, but those two should operate smoothly together whether the trigger is pulled or not.
Edit: Google says when the trigger is held rearward, the verticle extension is at a higher point, thus increasing friction against the safety plunger.