I've actually gotten my modded game running successfully on steam deck before. Like you, I added it as a non-steam game. The key to success in my case was changing some proton compatibility settings, try seeing if switching a different version of proton in your settings for the non-steam game will allow it to launch.
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Thanks for replying! So I tried that a few times, and even made sure to install the game internally, but I kept getting the same "Error Uncaught Error: Header is Wrong" warning over a black screen every time the game boots up, then it just stays stuck on that until I close it. Do you have any idea what the "header" may be referring to?