I conveniently had my UT04 retail box sitting on the shelf next to me. I can confirm there's a little penguin on the back of package, and under OS requirements they list Linux with an asterisk explaining it's not supported by Atari (publisher).

There is nothing else in the manual indicating how to use the Linux version, which disk to use, or any additional information that I can find.

Edit: geez I miss game manuals sometimes. All the game mechanics are so nicely explained, and it has instructions to setup modding tools!

You may absolutely be correct, I only learned of it a decade after I bought the game.

Still awesome to include a native Linux version of the game back in 2004!