I realize that this is a very old post, but I recently went through this myself so I’ll answer it. If you go into the dolphin settings (Main batocera menu > F1 > Applications > Dolphin settings), go to controller config, select the controller you want to configure, and clear out the L and R button assignments using middle mouse click. If doing a standard assignment of your triggers in the analog triggers section maps them as buttons, you can right click on the mapping buttons and it’ll bring up another window from which you can see all of your inputs. Find your analog trigger (they’ll probably be an axis) and assign it to your button by entering it into the text field below. Confirm out of the window and test out your triggers.
Hopefully this helps anybody looking for this in the future!