Or did you?
I remember BUYING Star Control 1-3 in an anthology when SC3 came out in the 90s, but it only came with a tiny manual for SC1 and 2, which didn't contain any of the answers to the CP challenges that randomly pop up every so often when SC1 launches.

Bonus question: How is it legal to sell UQM? Isn't it GNU GPL/Creative Commons?

The Ur-Quan Masters is based on 3DO source code. GOG sells, AFAIK, the original PC version of the game.

Also GPL/Creative Commons games and media can be sold unless there is specific NC (Non commerial) clause (I believe UQM does, like most originally retail based source projects, have this clause). Note that GPL/CC only applies the specific source fork provided by the devs, the devs could (with ATARI blessing as they own the rights now) release their own commerial fork. Obiously this would require them to make their own Windows port of the code without borrowing any new code (post source code release code) in UQM.

Edit: I see your confusion comes from GOG using game's original full name "SC2: The Ur-Quan Masters". I haven't bought the game as I see no point due to superior free UQM so can anyone who bought the game state wether it's the original DOS version or the native windows UQM?

GoG sells the original DOS Star Control 2, not Ur'Quan Masters.

Oh, I had heard elsewhere it was UQM, not vanilla SC2.

Any info on the copy protection for SC1, though? I probably won't be buying it, as I already own all three games - but that's always bothered me about SC1 so if the gog version has removed it somehow I may pick it up.

They removed the copy protection for SC1. You still get the questions, but you can type whatever you like.