I just ran a quick test-run and discovered that there is an interesting difference in Y coordinates between Overworld and Nether portals.
As you can see, standing at the entrance to the Nether placed me at y: 6.62~~
Immediately upon entering the Nether, however, I was met with a wildly different coordinate. I was apparently located at y: 71.62~~
Clearly, this can mean only one thing.
The Nether is in Heaven.
Anyway, I tried it again; this time building the Overworld portal somewhat higher:
When I entered the Nether at y: 11.62~~ (5 blocks higher than the previous), I still ended up in the same location on the Nether end. (y: 71.62~~)
From what I can tell, the Overworld y: coordinate has no effect on your y: coordinate within the Nether.