You asked two questions. Lets do the second one first.
NO ONE on here will argue against spiral up-cut bits getting all the crap out of the mortise simply as it is made to do that. NO clogging, no heating, no crap build-up in mortise, etc. These are not inconsequential issues Particularly if you are doing a run of 12-20 of them.
First…...........not sure why the worry about the bottom of the mortise being perfectly flat. You are going to drill a mortise depth that is a TAD longer than your tenon. Just a tad. And that will fill with glue, so if the tenon is not going to hit the bottom of the mortise, why the concern if it is flat. Note, I said a tad. Not 1/8 "bumps in the bottom of the mortise
But your Trend jig will take care of the bottom of the mortise.
May I show you a set of table legs, rails still, etc already for glue-up.
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