Hi Jonathan. Your URL example should actually be [https://www.wikitree.com/
wikitree], shouldn't it? I don't see any need to expand that one, because the full URL is already present.
For the WikiTree ID links and the templates, expanding them in place is going to produce quite ugly text. It might be better to add a list at the end of the biography as a key, indicating the translation of the templates to the full URLs. There are other advantages in leaving the templates present as well. They are easy to read, and could be useful in the future if the site in question changes its URL format.
Personally, I would prefer to retain the option to keep everything as it is at the moment, because I would use local software to turn templates and so forth into whatever form I wanted. I know this won't suit many people, so the proposal has merit. If there is a change, it will be good if the GEDCOM download page can provide a choice between the old and the new arrangement.