Yes, you can either add the game as a non-steam game and force proton, or use Lutris or Bottles (with proton or other WINE runner). For repacks with installers, you can launch the setup.exe with Lutris or Bottles (install the game to 'fake' drive_c and move it), just make sure you include dependencies that require it (usually .net framework).
Source: most of my steam library on my steam deck is plundered loot