Zack
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Zack's post in SSEEdit - Only listing default Skyrim files - No mods listed was marked as the answer
Edit: I managed to get it working.
Due to Elysium using a "Game Root" folder, I copied SSEEdit and its related files into that directory, updated the path to it in MO2 and ran it. It can now successfully detect my mods. Not the best solution, but it works.
Hope this helps anyone else in the same boat.

