Honestly Minecraft is so eerie because of that loneliness. I have always seen the “story” of Minecraft as Steve’s fruitless search for other survivors, wandering the landscape, following maps and unearthing ruins and hoping to signal to someone else—anyone else—that he is here, that he’s alive.
For example, the Beacon has obvious utility for the player, but in the story, it seems much more like it would be built as a signal to others.
It is made more eerie by the fact that the creatures he encounters are misshapen mirrors of a human form. The villagers are clearly evolved either from humans or a human-like ancestor, but are not themselves human. Drowned and Zombies perhaps were once human, but unlike zombie villagers, it seems that they cannot be cured. (Maybe he will find a way. Maybe, maybe.)
The Endermen are peaceful when respected, if unnerving. They used to frighten him, but he has been alone for so long; the empty horizon that once held hope has become so unwelcoming that the garbled syllables of these flitting black figures are almost a comfort. He talks back to them, seeing patterns in the handful of noises they repeat that aren’t there.
He has followed the clues left in the ruins, piecing together doors to the hellish, inhospitable realms the previous inhabitants of this world must have tried to escape to, and encountered incomprehensible beings. He has discovered weapons and ancient texts imbued with magic and learned to replicate it.
It has been so long. He has traveled so far, from the harsh, unforgiving lands of the desert, over mountains and into sticky jungles, and there is never a new clue, a new signal, something, anything left that might indicate that there are survivors.
So what would he think, if he saw someone appear, standing in the doorway of the fortress he has built over the years, someone human? Someone else, after so long spent searching? After so long spent knowing, deep, deep down, that there is no one else left?
What is more likely? That he would think this is a surviving human, incomprehensibly, after all this time?
Or that this is yet another being, in a world of magic and strange power, that once was human, or is trying to be human, or is not quite human, that is just
better than the others at pretending?