This is exactly right. Remapping them in the config for the actual core can achieve the result of the buttons mapping correctly for game play, but outside of game play it makes navigating the Retroarch menu use different buttons than the other emulators. The fact that the core option for re-mapping buttons is there and works but doesn’t actually let you save is such a horrible tease!
Reply To: How can I use core-specific button remapping for Retroarch emulators? 3.0 beta 2