There is no connection between the internal and external stems. Nor are they mutually exclusive. That is he first time I have ever heard of mortising them. I can't see any useful purpose.

The internal stem makes construction a lot easier because you don't have to fiddle about getting the ends of the strips to meet neatly. You have something fairly substantial to glue the ends of the strips to.

The external stems also make construction easier and if you use hardwood, they help the bow to resist damage from minor bumps. With an external stem, as long as the strips reach to the outside of the internal stem or a bit further, all you have to do is plane them back either until they are neat or until they are as wide as you want your external stem. Several laminated thin strips of hardwood is a good way, but not the only way to do them.

I can't think of any reason to attach them after glassing the hull. It sounds like extra work to me.

How far back from the bow the external stem goes is very flexible. If you want a lot of protection for the bow when you run up on the beach, you might make it quite long. Same thing at the stern. If you have made it from hardwood you might want it fairly long if there is danger of scraping the hull on the bottom on shallow water. So the answer is usually somewhere between 6" and 18". You decide.

A generously deep external stem on the stern is a good, unobtrusive way of getting some of the benefits of a skeg. Another good thing about doing it that way is that it is easy to plane it down and glass over it later if you decide it was not a good idea. I fitted one on my wife's kayak and she loves it. I don't want one on mine. Once again, you decide what sort of handling you want the kayak to have.