Isn’t the nether above the overworld?

Overworld, Nether and End are completely separate, coordinates 12 34 56 in the Overworld are somewhere else than coordinates 12 34 56 in the Nether.

I don't think even in Christianity hell was originally supposed to be below and heaven above, it's just usually associated with that nowadays. Someone please correct me if I'm wrong.

There is an X and Z axis which corresponds to North, South, East, West and the Y axis is for elevation. You can have an elevation of 50 in both the Nether and in the overworld because the coordinates are relative to the dimension you are in at that time.