I think you are over-confusing something that's really simple.

Along the path of strip building boats: people used to strip canoes and kayaks and have the strips meet at the end of the boat with a zipper of strips. One strip would overlap the one on the left side then on the next row, the left side would overlap the right strip. Then this entire zipper of strips would be sanded or cut off and shaped to the smooth ends of the boat. It took more skill and work than using an outside stem.

Then a genius came along and and figured that if you run strips to the end of the form and just cut them off flush, it would be so much easier to just cover that blunt end with some wood (outside stem) and it would be stronger as well.

Whatever boat you are building that's the principal. Your inner stem is usually the end section of your bow and stern forms. Often the outer most part is stapled or fastened in some way so the "inner stem" just stays in the boat and gets coated with epoxy. I would contact the designer to clarify what the intentions of the plans are if it's not clear on the instructions or wherever.