the only thing that wasn't working {for me at the very least.} were the direct downloads from Nexus via MO2 but that's inconsequential since you can always just install the mods manually.

but yes, MO2 works perfectly in Wine/Proton. it's especially easy to set up a shortcut to it using Lutris. for example, installing New Vegas using the GOG install script and then editing the settings to replace NV's executable with the MO2 executable.