Looking at the last screenshot, your ROM folder are named differently than what EmulationStation is configured to look after (snes, saturn, megadrive, etc), so they're probably ignored.
From your mounting schema, I see you're using a FAT32 drive and you're trying to mount the whole /opt/retropie (!) on it, under the pi user. This is not correct and it's going to cause issues - you shouldn't do that. And probably /etc/emulationstation should be left also alone - if you want to edit it, just create your own customized es_systems.cfg in $HOME/.emulationstation/ and use it.