I went back and reviewed the video again. At the 41:32 mark is where I guess I got confused. It says games with the default config must be used with the FS-UAE emulator and games with the custom config must be used with the FS-UAE UUID emulator. This threw me off as I wanted to tie the exporter to custom config games for some reason.
So just to clarify for me, the UUID is specifically used where you have multiple versions of the same game name and you want to launch a specific version, is that correct?
For my purpose, I don't have any game version duplicates, and I am not using FS-UAE UUID emulator entry, yet I am able to launch my custom config games using the FS-UAE emulator with no issues. According to the video, this shouldn't be the case. I'm just trying to figure it out for myself. The video is very thorough and quite long. I'm sure I'm just missing a few pieces of the puzzle.