I'm running into an issue with a 320x240 ILI9341 screen. It's adding top/bottom black areas, which affects all of the emulators, but emulationstation is displaying perfectly. In config.txt I have the overscan disabled, all of the overscan_left/right/etc commented out. When I set the framebuffer_width=320 and framebuffer_height=240, it squashes the console text just like it does the emulators. If I leave those commented out, the console text works at fullscreen (but very small). I've tried changing the screen width/height/offsets/etc in retroarch but haven't been successful in changing the behavior. This is in RetroPie 4.4 on a RPi0w with display_rotate=1 to make it landscape.
Emulation Station w/ GBZ35 theme:
Game Boy Color:
Atari 7800:
Maybe the fact that the Atari emulators compress more than the Nintendo one will help us find a solution. Atari should be using the full 4:3 aspect ratio, while the GB/GBC should be 240x240 with an X-offset of 40. Plugging those into retroarch doesn't seem to make any difference, so I'm not sure what I'm missing. This is a stock 4.4 image so there shouldn't be any overlays either.