Simple Mods can be done with WASM, so you can compile basically in any language for those. and even more simple mods just need CSV Files to contain their Stats.
NPCs react to each Player individually, so it is difficult to say what you mean with that Question. Even Minecraft Villagers store their “relationships” per Player.
You can compose your own MIDI Music and put it on a Music Disc. Kindof how EthosLab faked it on on his recent Hermitcraft Episodes. (he edited Noteblock based Music into his Videos).
Forcing contact with Hazards means that you need some way to automatically defend yourself. There always needs to be a way to avoid Mobs.
As for the Space Stuff, while I will design the World to be explorable in Space, the Tech for it will likely be added by Mods first. The “Skybox” will actually not be a typical Skybox, it will accurately show the visible Stars from wherever you are on the Planet.
Minecraft and uhhh, I dont think there is other Games I know that could be comparable, apart from GregTech. Maybe Morrowind a little, when it comes to the Stat System and Inventory.