Bumping this because I have the exact same issue with a Hyperkin Admiral. Batocera utilizes the R Analog inputs as the C buttons within the N64 emulators. If one is using an N64 type controller with actual C buttons, Batocera makes it impossible to bind C down, because it only asks for R Analog Up and Left (C Right works because it utilizes button A I believe)
If all 4 directional inputs were available for R Analog when binding controls, this issue would be fixed.