For the steam deck, I would recommend not using the windows version, and instead making a dedicated linux port, I've tested NWJS 49.2( linux version ), on an MZ game, and it works perfectly on steam deck( and my laptop, which also uses linux ), imo, there's a lot of inconsistencies with just relying on proton for porting an MV/MZ game to linux. I.E. some weird graphical glitches upon soft reset, frequent stutters, and more frequent crashes, as least from my testing.
Also porting the game to native linux/mac is really not that hard at all. It's definitely worth the small amount of effort imo ^^; All you gotta do is replace all the NWJS files from the project with the linux ones nad it'll be a native linux version. The ONLY thing you'll need to worry abiout is the consistency of your file names when porting to mac/linux( unless your doing some really abstract Node or NWJS specific calls in yoiur game, which is very highly unlikely ).
For example.. In windows If you have a file called "Hero_01.png" but some plugin is hard coded to accept the file "hero_01.png", windows will have no problem finding the file correctly, but linux and mac are case sensetive file systems! Which means that... because the plugin is looking for "hero_01.png"( all lower case ) but the file is actually named "Hero_01.png"( the first letter is capitalized ), linux and mac will NOT be able to find the file, so you'll end up with an error telling you that the specific image is missing, all it would take to resolve this issue, is change the file name from "Hero_01.png" => "hero_01.png", and do the same for any hard coded file names. It works like this for ALL files, and folders in linux, any file or folder, the spelling MUST be exact!
However in most plugins, it's not common to hard code images, or audio names, so in most cases, these type of occurences would probably not ever really occur, so in most cases it's just a matter of replacing the NWJS files.
Sorry for the rant ^^; but as a native linux user and a steam deck owner, I thought this advice would hopefully help others who plan to add support for linux/steam deck, as it's FAR easier than one would think, even for MZ which doesn't have a native linux export option like MV does.