Well, the behaviour is great if you're using markers only as short-term working "notes" and always ticking them off when you're done (use favourites for places you want to save longer-term). But yeah the marker feature doesn't explain how it wants you to use it.
I use the markers to loosely transcribe walking routes from books or the web then tick them off during my walk. I was always curious if this is what they're actually designed for, though.
I most commonly use them for marking the location of my car or campsite when going bushwalking and wanting to be certain I can find them again. Also sometimes for marking annotations I want to add to OpenStreetMap later...