The gear up rationale is based on the KISS principle and a desire to avoid touchdown bounces.I wonder how far they’ve tested that. Some aircraft will ultimately disconnect the autopilot if not correctly configured for landing and at a very low level. Be a bit sad to be looking good, but then at 100’ have the autopilot dump it back into your hands, and very likely with a strong nose up out of trim situation as well (because some aircraft put in quite lot of nose up trim, as a safety measure in case of accidental disconnect). I see no reason not to put the gear down. The autothrottle will handle the drag change, and if you’re worried about the braking side of it, then many have some form of autobrake, which is a very simple dial selection.
The possibility of a late, low unexpected autopilot disconnection like you describe would not be ideal and is something I’ll ask about.