I thought about it a bit, I think I would like to keep it within the main world and not in the nether. Partly because I don’t have a good understanding of the nether.
A nether block is equal to 8 surface world blocks, so distances are 8x shorter there. To correlate portal coordinates, divide the X and Y surface coordinates by 8 to get their respective nether coordinates. Height was the same, but not sure how coordinates above 128 are handled now.
On the pro-nether side, 8x less track and track base.This adds up over longer distances. With an 8x shorter distance, both rail and foot traffic are 8x shorter and faster. This will also create easy access to nether fortresses, and other fine nether features. Putting in a couple rows of glass in the non-tunnel stretches makes for better viewing than being completely underground.
On the con side, you’ll need to completely enclose the tracks when not in a tunnel, due to mob attacks. This will require a fair amount of cobble, or whatever. Will also need to create portal pairs at the stations, and coordinate their locations, which is actually pretty easy using the above method.
Thats my $.02 on it.
About correlating nether/surface portals; If there are other surface portals within (IIRC) about 300 blocks, you might pop out there if your nether/surface portals coordinates don’t match.
Nether height. I’ve had a lot of success with running roads/rails at levels 70-80. There’s a fair amount of tunneling, and also some large open areas. Was seeing a lot of nether fortress road systems around level 70.