I had tried to edit that file but I really don’t grok what I’m seeing in there. But I think I have it working now based on that second link.
In case others have this problem, in MBGA, load a game, and then hold down Shift and press MENU. That will bring up the QUICK MENU.
Use the D-pad to go down the list to Controls and select that (with A if you’re using the Xbox layout). D-pad down to “Y button”. Don’t use A to select that, but rather use the D-pad right button until you see “R” selected. Be sure that reads “R” and not “Right”.
Those are different things.
Then D-pad down again until you see “X button” and change that in the same way to “L” (not “Left”).
Then D-pad up to near the top of the CONTROLS menu and then select “Save Core Remap File”.
After I did this, things started working as I expected.