protonhax VS steamtinkerlaunch

Yes, see https://github.com/jcnils/protonhax

On Steam, since it uses Proton, the only way of running an .exe on the prefix would be using ProtonHax.

I've used Cheat Engine with Elden Ring. I used https://github.com/jcnils/protonhax to run CE within the wine instance started by Proton. But I think I used the x86_64 version. You specifically talk about a speed hack. Have you tried other cheats? If it's specifically the speed hack that doesn't work, it may be broken with the current version of whatever game you're trying to hack.

How did you install cheat engine? You need to run it in the same proton/wine prefix as your target process. I use protonhax for steam games, but there are other ways. If you're targeting native linux processes, look into ceserver.

try protonhax, it works with bakkesmod

Using protonhax, I got CE to work.

I haven't used it myself but steamtinkerlaunch is definitely your best bet. It lets you easily set up Mod Organizer 2 or Vortex directly on your Deck. The quite extensive wiki will provide more information than I possibly could.

For any problems, suggestions and contributions you might have, please use the issue tracker (which was the preferred way already before)

Tinker Launcher is the easiest way to do it. There is also a third party Linux "port" of MO2 you can install. Tinker Launcher is my preferred method. ProtonupQT is not where you get it from. https://github.com/frostworx/steamtinkerlaunch/wiki/Installation

Another app / set of scripts I have found is https://github.com/frostworx/steamtinkerlaunch.

https://github.com/frostworx/steamtinkerlaunch/tree/mo2-overhaul branch.

Yes you can use mods/mod managers with Steam Tinker Launcher