as a mod i have access to information about user accounts. i know you're the same person. i also didn't ban you. anyway, onwards:
That guide has two parts, automatic is great when it works, but it doesnt include an fstab setup. If for other reasons you need to mount that drive later in fstab, doing so does break retropie because you cant use /mnt/usb.
i don't see why it would break retropie. one of the manual steps is to disable the usb daemon, so automatic method is disabled. the manual guide doesn't tell you to mount on /mnt/usb.
some systems can handle subfolders apparently, but for mame and (evidently) psx, try:
https://github.com/RetroPie/RetroPie-Setup/wiki/EmulationStation#custom-collections
Nice, but why didnt you bring this up when the OP made clear his initial problem was trying to sort his collection?
i don't think "OP" made it particularly clear, but we got there in the end. you'r.... they're very welcome :)