Ashley No worries, thanks for the thorough response. I appreciate the consideration being put into this and am seeing myself why it's a bigger feature than it sounds.
I am definitely a proponent of methods 2 or 3. I'm not exactly sure how there isn't a way to tell a rename apart from a delete-and-add - I would assume finishing either operation could or would send a particular signal to differentiate, but evidently not.
Overall method 3 sounds just like 2 (my favorite option) but with a dedicated rename operation to solve this so... Unless I'm missing something I say that's the winner!
Even my current project has 18 "area" layouts with far more layers than I care to deal with, so this feature will help immensely. For level-based games in the future it is an absolute must! Thanks again for considering it and I look forward to seeing how it plays out.