I recently bought expansion packs and now I have two games in my library - original Witcher 3 and Game of the Year Edition. Are they different in any way(should I download both for archiving purposes, or they are the same)?

Thank you for your response.

Heres a remnant from the past. Im bout to revive a post from 2017.
So when and how was the GOTY game gifted just curious? Ive had this game forever & havent played it and just thought it might make more sense to start playing the GOTY version instead of dealing with a slight hassle etc

The GOTY was (and perhaps still is) gifted to anyone who owned the base game and bought either the expansion pass or both expansions seperately.
The GOTY gives you the option to play the fulli game, the base game without the expansions, or just either expansion.
So far I only started a full game. Personally I prefer to not start the expansion quests other than grabbing the note from a notice board.
If you play the full game, the north eastern part of the Novigrad area (not the city) is expanded by the Heart of Stone expansion.

To give you an idea, you can check the maps without and with the HoS expansion:
http://witcher3map.com/ (without HoS)
http://www.tivaprojects.com/witcher3map/ (with HoS)

If you want to start the full game but stay away from the expansion areas and quests, you could use this quest list.