I'm posting these same instructions to now, and linking to this ticket.
Download mods from and extract them in steamapps/compatdata/839770/pfx/drive_c/users/steamuser/My Documents/My Games/Phoenix Point/Mods. Open a terminal to steamapps/common/Phoenix Point/PhoenixPointWin64_Data/Managed. Install mono and basic assemblies, version does not matter. Extract the file Modnix.exe to steamapps/compatdata/839770/pfx/drive_c/users/steamuser/My Documents/My Games/Phoenix Point/Mods (you need to create some of those folders). Extract the files in the Managed folder in the 7z file (3 DLLs + 1 EXE) to steamapps/common/Phoenix Point/PhoenixPointWin64_Data/Managed (no files are replaced). Download (or a later version, make sure it's the manual setup one). 
Also, use proton 5.21-GE-1 or proton 6.0-GE-1 to run it. (Obviously make sure you run the game once before doing this. So to install mods on Phoenix Point: Year One Edition on Linux using Steam, I worked out some instructions:
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