When making custom furniture there are a few basic rules that will
always help in ways that are always surprising.

Rule 1, always cut things very very square.
Rule 2, always mill all of your stock to the exact same thinkness as a
group, ie 4/4, 5/4, etc. with plenty of extra as a starting point.

Now, when cutting tenons with a jig on the TS use some scrap (of the
exact thickness of final piececs) and setup jig so using a dado blade
with two passes (cut, flip, cut) you create a tenon, (exactly centered
automaticially) of the appropriate thickness. You'll need to use a
backer to keep from blowing out the backside.

Yes, cut the shoulders by hand, or router. I use the router table with
a fence. Lay the piece face down and up against the fence and push it
straight into a bang or spiral cutter. Just take an 1/8th or so and it
works ver nice. I setup a stop about an 1/8th in short of the shoulder
and chisel out the last little bit. Can do the same with the TS and a
sacrifice fence with daod or no casrifice and regular blade set 1/16th
from the fence, but I don't like backing off of the TS blade and harder
to stop, although you can setup a stop outside the blade. Looks
dangerous though, so that's always my first clue.

Now when you set your mortises in the exact location you desire, you
know exactly where the face of your stock will be as long as you work
everything off of centerlines. And knowing you have exactly square
faces, everthing sucks up real nice.

This is all opinion of course.