Thinker Mod SteamDeck
I'm happy to report it's quite easy to get the Thinker mod (v5.5 at time of testing) working with Alpha Centauri on SteamDeck.
Here's how: Switch to SteamDeck desktop mode. Download the mod. Extract to the Alpha Centauri folder (found in /home/deck/.steam/steam/steamapps/common). Rename terran.exe to terranold.exe. Rename thinker.exe to terran.exe. Switch back to handheld mode. Get Alpha Centauri to launch Alpha Centauri Planetary Pack (NOT Alien Crossfire, you might have to go into the steam options to change this if you have it always launching to SMAX already). You are now playing Alien Crossfire with the Thinker mod! It also still shows you as playing Alpha Centauri and logs your hours.
This is notable because according to the author, the mod is really only tested on Windows on the GoG version of the game. I played for a few turns, seemed to run great. Will have to play more in the morning.