Well, my 8bitdo SFC30 seems to work ok in Kodi and ES. I saved mappings through Retroarch (I see it in .cfg), but it fails to work in games. Actually usb gamepad also stopped working, so i cant even exit games...
Ill play around with .cfg i gues and come back with what i find out.
In any case, sounds like you need to adjust your TV to "just scan" 16:9 or something along those lines. Normally, Kodi and Emulationstation should pick the optimal resolution for you (normally 1080p). There aren't any resolution options in ES as far as I know, it will just use whatever your X server is set to.