If the end of the tenon is going to finish flush, I would leave it proud a little and then plane if smooth with the surface after the glue dries. If the end of the tenon extends out as a finished product, I would at least put enough finish on it to seal the exposed end and prevent glue being absorbed so the glue can be easily wiped off while wet (this is assuming its a water soluble glue like tite-bond). If using stain, apply the stain and one layer of top coat on the exposed portion and back slightly into the joint area.
When I draw bore a joint, I go light on the glue, so as not to gum up the draw-bore hole, putting no glue on the tenon in a strip from the end to the hole, and just applying glue to the top and bottom thirds of the mortise. Glue can go on the peg when it is installed.
If the tenon is a snug fit, just putting glue on the sides of the tenon and hoping it spreads may end up with a glue-starved joint for most of the tenon length. If the tenon slides in easily, that method may work better.
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