Al Breed replies: I align mortises with tenons by using a marking gauge set to the mortise width and referenced to the outside of the piece. Using these marks, I cut the tenons on a dado blade or by hand, and set the mortising machine to chop the mortise. This way, the outside of the joint will be flush and any difference in wood thickness will be on the inside of the piece.
In joining a table skirt to the legs I leave about a half inch shoulder at the top so the tenon isn’t exposed at the top of the leg. The bottom of the skirt has no shoulder in order to make the tenon as long as possible. Some antique work has a variable shoulder on the inside that corresponds to variations in stock thickness, but the outside shoulder is constant, having been set with a marking gauge. The driving reason in sizing tenons is maximum gluing surface – shoulders provide stability against racking, so you must balance the two.