I think this is really overblown. It only matters when you see someone's handle posted elsewhere. When you discover them naturally in your timeline you can just follow them. It could be solved with a new URL protocol scheme easily (instead of linking to your account on your home server, create a link to your handle on its own: fedi://@myname@myserver.place)

The reason it's confusing currently is that people link to their home server, which is not useful to someone trying to follow them.