Subnautica runs excellently with WINE and Steam Play Proton, and mods work with such a setup as well.
The following are instructions on how to set up Subnautica with QMods and get started.
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Install Subnautica via Steam Play/Proton. It should run out of the box with DXVK; however, you can check for any issues on ProtonDB
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Download the latest QMods ZIP release (Manual Install) from Nexus.
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Unzip the file into
~/.local/share/Steam/steamapps/common/Subnautica/(or wherever is the data dir is).