I am afraid it is not possible to “let the core” do the rotation within the Mega Bezel.
I have done a “Book” standard overlay, (Only works with melondsds.) I just haven’t updated the repo yet.
My koko-aio pack has a book graphic (based on the overlay) that can function as a standard overlay.
There is a lot of discussion in the discord retroarch development channel about defining screen bounds and orientation in melondsds when a border shader is used. Not sure how they will handle d-pad rotation though, or when any new code will be finished.
There are a lot of systems on my to do list. (When I get back to it.) Any additions to finished systems will be a lower priority, if they happen at all.