It seems like if one has been above the nether and other mobs can spawn then rifts will spawn above the roof as well.
Perhaps a fixed limit on where rifts can generate between certain y layers, like no higher than roof -3, no lower than laval lake?

Just to be clear, you're referring to Flux Rifts added by base Thaumcraft and not Dimensional Fractures, correct? But anyway, I thought rifts were set to appear at the lowest location they could in the nether instead of highest for this reason. Although if there is no valid spawn location under the roof, I wonder if it would be able to spawn there...

Thank you for the response.
To clarify, it's the dimensional rifts from this mod which once can open with impetus.
It seems they can spawn naturally above the Nether roof.
It seems when they spawn above the roof, one can pass through from Nether to Emptiness, however when trying to go back, or for any rift opened from the Emptiness back to the nether it seems that they get the error message saying they don't seem to go anywhere.

Flux Rifts from Thaumcraft spawn as you described in a survival world at the lowest open air block available.

I did further analysis (which I should have done before reporting).
It looks like it might be caused by a mod that removes the nether roof, called Better Bedrock Gen as such there's no bedrock level if this mod is looking for it.

I originally installed it as a QoL addition to the overworld, not realizing it'd affect nether generation.