While using command blocks in the nether, it isn't possible to set spawnpoint there like you can by having a user type /spawnpoint.

For example, if a user types /spawnpoint 100 100 100 in the nether, when they die, they will spawn at 100 100 100 in the nether. However, when doing so with command blocks, they will spawn at 100 100 100 in the overworld instead.