The obvious cause of glue squeeze-out in joints is that too much glue has been applied. So the obvious way to avoid the squeeze-out and resulting splotching under a stain or finish is to apply less glue.
As shown in the accompanying picture, you can countersink a mortise and a dowel hole to create a reservoir for excess glue to collect. You can also chamfer the ends of tenons and dowels. Most dowels are manufactured with the ends already chamfered.But you don’t want to apply too little glue either or you won’t get a good bond. So here’s a trick to give you a little leeway.
Another precaution you can take is to cut the mortise a little deeper than needed to allow excess glue to collect and drill the dowel hole a little deeper than needed for the dowel.
Unfortunately, there’s no easy equivalent for stick-and-cope joints on cabinet doors.