You will be very happy if you drill the mortice and after fitting the sections pricking the peg location, turn the drill backwards, pull apart just enough to access the tenon peg hole, off set the tenon peg hole, for the most part a tad closer to the shoulder. Braces are a little different, still closer to the shoulder but away from the but end. This will ensure pegs are pulling joinery together and not pushing apart. Doing it now in the shop means you won't have to pull out a drill during the final assembly, one more thing you won't have to do on a busy day.