Have you tried installing MTGO using Lutris? Apparently it works fine, but you'll need some tweaks. The key is to use windowed mode, disable music and card animations:

Runner options: -Use the latest version of lutri-proton if it's not the default. -Use windowed (virtual desktop) mode and the display resolution of whatever device you are playing on. This was the biggest fix of most problems for me with stuff related to proper rendering of windows. -All else is default from Lutris install

System options: -Uncheck restrict number of cores -Disable desktop effects -All else is default from Lutris install

In-game options: -Disable or silence music and Uncheck play client startup music -Disable card animations(summoning sickness and foil treatment)

I've also found that it is always better to close the program using the Stop button on Lutris, there's a bug where sometimes if you close out of the game via the Close button in the window, it will not properly stop the game, and will prevent starting the game back up again. I also tend to start the game in Lutris instead of via a desktop shortcut.

https://old.reddit.com/r/SteamDeck/comments/101262d/psa_mtgo_on_steam_deck/j9bqck9/