Since this is still a really good game and I still play it. I found a way to make it work with both the Steam Deck. I've patched the exe to enable 3D (essential for the steam deck) along with the patch that had already been done by Pete Jatz. Both version are pretty much the same except the Steam Deck worked straight up with rdoeffinger's latest xwa_ddraw_d3d11 (you may or may not have to add the ddraw to protontricks winecfg, I added it to be sure: see here:

Running TIE Fighter Remastered on Linux
A Guide for STAR WARS™: TIE Fighter Special Edition
By: twm77
Getting this old game running well on LINUX using proton was a bit of challenge. This guide focuses on getting the remastered version working, which by default seems to crash as you enter the missions.
if you want to replicate that step if you need to.

This post serves as consolidation of what I hope were many fixes scattered around, mostly by Teleguy's good work.

Steam Deck:
https://www.dropbox.com/scl/fi/z5tz1mtpv6cg5f9tqvr8m/TIE95_REC_3D_SteamDeck.zip?rlkey=yzit95f1z7b0zeudva4oyvub2&st=4zvpbst9&dl=0