Don't have a steam deck, but I do run a pretty similar linux setup on my regular PC.
Great info with a tool I've not seen before, thanks for sharing.
A few further tips:
you can use any other BitTorrent client other than transmission. If you use it on windows, it's likely it'll also be available on linux too. I like Qbittorrent personally.
You likely don't have to use lutris to add the installer. If you already have wine installed, you should just be able to right click the .exe and open it with wine. To help a bit with where to place the game, the Z: drive is your normal linux file system if you want to change install location, which I reccomend to make finding it easier
Always say no to updating or installing directX versions. We don't need them here.
If you have issues like it stopping half way through, try pressing the "limit to 2gb of ram" button.
Of course, check protondb if you find any problems.
Sometimes, like with RE4 adding the game to steam as a "non-steam game" can be a good idea. In steam, it's on the bottom left, a small plus button. No idea on the steam deck how to do that though. You may have to go into properties and force comparability. Of course, do so at your own risk.