Yesterday, July 1st, they announced the Alpha release of this next-generation mod manager and their new Product Manager got in touch to mention they “would be really keen to get feedback from Linux users”. So this is your chance to ensure Linux (and Steam Deck) finally become a first-class citizen for game modding.
Does it work with nonstandard steam directories and proton?
Worst case scenario you could just bind mount the nonstandard steam directory into the usual place
It only works with Stardew Valley right now, but a gog and steam are support so I think you can point it to where you have the game.