Why is GOG's version only in English, while physical versions have many other languages (French, German, Spanish, Italian and even Japanese)?
GOG should really add these languages in their preservation program

Agreed. I have both Alpha Centauri and Alien Crossfire in the Spanish physical release, and both are fully translated (text and voice). And I must say, the dub work is fantastic.

So GOG, is there a copyright issue with the localized versions? or is a lack of availability of the files from the developer? Is there any way in which those languages can be added?

There's a Russian translation on zoneofgames .ru (can't post links for some reasons, sure you can find it if you just search for the name of the game)

mon ami, links from that post do not work anymore - is the French translation available somewhere still?

Pretty sure it works.... https://www.gog.com/forum/sid_meier_s_alpha_centauri_/fr_alpha_centauri_une_traduction_complte/post26

I just checked all URLs from the opening post, and they still work well.
Could you be more specific about what does not work for you?