I bet this has something to do with them being sold off last year and the new owners not seeing the cross platform app as being worth it

In case anyone wants it, you can get Vortex working with WINE games. It's a pain, and it does have issues, but it can be done. I've only ever seen people say it can't work, but you can run it under the same prefix as the game and have it function 95% of the way fine. There will be some warnings that won't go away though.

Ahh looks like this is not going to overtake Mod Organizer 2 anytime soon, sorry for not checking before crossposting!

Huh, is there one that does Stardew Valley?

Just use Wabbajack. It does the same thing without being directly tied to Nexus

Jackify is a native Linux tool that downloads and installs Wabbajack modlists, and creates a Proton prefix with needed tweaks.

https://github.com/Omni-guides/Jackify

I've used it to run a modest list of Skyrim mods (100ish), and it worked pretty well (although Requiem was very difficult, and I ended up not being able to fully install it). There is a bit of a learning curve, and the wiki provides a decent introduction. It doesn't cover every single use case but is enough to get up and running. No virtual file system like MO2. It makes a directory for all installed mod files, then drops those into your game files when the mods are deployed through Limo.