1. That is a slightly undersized tenon but I wouldn't worry about it.
In case work, like end tables, derssers, etc, you aren't going to get
the kind of work stress you would in a chair or entry door.
2. Just cut the tenon short, end grain gluing adds no real strength. In
your case, just make sure you stop the combo panel slot/mortise so it
doesn't run out the end of the stiles. You'll have to plunge it on the
router table to get it started but no big deal. Having tight face to
face grain on the tenon to slot mating will give you all the strength
you need. Also, I prefer to run the stiles long and the rails wide and
worry about getting the interior of the frame square and to the right
dimension, then trim the framed panel down to size.
3. Since you have such a nice saw, just get some MDF and a few bolts
and build a dado sled. I'll actually have a nice design for one for
myself in a few days, it's just in my head righht now. You can do you
tenons laying flat on the sled for the face cuts and on edge for the
4.I prefer setting up the TS for precision work. The router is just not
as consistent. This may just be me but I've tried bot a lot and only
use the TS for anything that matters. Although I'll get my Leigh M&T
eventually, or maybe even a MultiRouter.
What material and finish are you using?