I had written about this in their Discord in a thread:

using this shim script I made, do the following:

1. Install Raft with Proton 9.0-# prefix
2. Place the shim file into the game directory
3. Mark the shim as executable
4. Set Steam launch options to: WINEDLLOVERRIDES="winhttp.dll=n,b" ./shim %command%
5. Launch Raft once
6. Place RMLLauncher.exe into Raft game directory
7. Look for a plaintext target file that should be created in the raft directory
8. Copy the location of the RMLLauncher.exe (exact folder and filename) (right click > Copy Location in KDE / Steam Deck desktop mode)
9. Paste this location into the target file and save
10. Launch Raft
11. Go through RMLLauncher first-time steps
12. Press Play
13. Stop the game and add mods into Raft mods folder
14. Launch the game and load the mods in-game
15. Play Raft modded through Proton

(Instructions adapted from both mine and Discord user YumiChi's)

This method doesn't require custom installations, messing with bottles, nor wine runtimes other than Proton.