Steam Deck is downloading the Windows version of the game instead of the Linux version.

[Hi-Tech Lo-Life]

I can confirm this as when I check the local files, I see that there is a bunch of Windows related files and an .exe file.

Tried using the steam console to download from the Linux depot but it tells me I'm missing a license for said depot?

[icehat]

you don't have to use the console to use alternate runtimes, just go into the game's settings > properties > compatibility > tick the box and select the native runtime

the deck will usually pick proton as the default. ironically native linux builds tend to be less stable than running it in a fake windows environment since linux is (by most developers) considered a second-class citizen. causing problems such as missing or broken cross-OS netplay (borderlands 2 is an example)

[Hi-Tech Lo-Life]

Unfortunately that option does not pop up.
https://i.imgur.com/y9ixHYp.png

Also curiously enough on a standard Linux desktop when I select Mosa Lina, this shows up...
https://i.imgur.com/7QIK9qs.png