Seconding this. And as another lemming said, moving a working setup from a Windows system can make your life easier. But once you have MO2 running, most mods can just be installed in it like normal. Though SteamOS makes it more trouble than its with to auto download mods via mod manager. Easier just to use the manual download option and then manually install it. (I set my MO2 downloads folder to be ~/Downloads to make my lifer easier on this)
Also, there is a Linux specific version of the 4GB patch. You have to make it executable and run it in the terminal to actually get it to patch.
You can run things like the BSA decompressor using proton tricks.
Or you can just run the 4GB patch and the BSA decompressor on a windows install and then copy the whole FNV folder over to your deck (overwriting files). That works too.
If you are a TTW kind of guy, do that on Windows, making it an installable mod, and then just copy that over. And do it before the BSA decompressor, or you will need to make a clean install of FNV.
Honestly, if you install MO2 using the link Headbangerd17 linked above, you can pretty much just follow the
Viva New Vegas gude. Just use protontricks for the BSA decompressor and the Ultimate ESM fixes things, and the linux specific 4gb patch. Or again, do all of it on Windows and copy over the game folder and the MO2 folder.
P.S. Its possible to get a complete setup on the deck alone, but if you go that route, it will save a lot of time to plug in a keyboard, mouse, and monitor. Or pair it to your work computer via SteamLink and do it while you're supposed to be working.
P.P.S
xLODGen can be added to MO2 and run on Linux just like it can on Windows. Though the SteamDeck does take a long time to actually generate LOD, so best to do it in chunks to make sure it looks good. It's really sad when all the rocks look like stretched buildings after you waited for all worldspaces to generate. Trust me.