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.
I realized I can use my USB2-A meter to test the output from the USB2 ports. Problematic PSU causes it to have 5.3V and the better one has 5.1V. Hopefully it helps anyone else having problems with a stronger PSU.
@windg usbmount is included in the image, but not in the manual installation. if you install via a manual installation, as it appears you have done, you will have to manually install it after the fact via the packages menu.
there is a package available upstream for both cosmic and bionic, would it be possible to maybe fix the script to not add the broken repo for cosmic?
The repo is mainained by the FS-UAE author and it's the recommended way to install it (https://fs-uae.net/download#ubuntu). If anything changes regarding that, we can also update the script. While for 18.x the latest package is upstreamed (Ubuntu), for older releases the PPA has the latest version. Let's see what happens when 19.04 breaks loose.
Incidentally, blkid still shows the drive (/dev/sda2)...?
blkid shows you the block devices detected by the system, but that doesn't mean they're mounted and available. The mount command should give you the list of mounted (and available) drives. I guess your drive is not automatically mounted at start or there's an error mounting the drive - check you by manually mounting it and see if any errors show up.