No idea if you can fix this, or if it's just an issue with the Atum 2 mod. So, basically, after entering the atum dimension and setting a waypoint, I accidentally broke the overworld side of the portal. Directly the below the portal had mined out the anti-matter. When I entered the atum dimension via my waypoint and went through the portal to regenerate the overworld half, it generated at bedrock, with the bottom layer breaking the bedrock. Turns out, if you break the portal and regenerate it, it breaks another block lower of bedrock. I tried this several times and it continued to happen. Pretty fun.

It just keeps going down. I have to build a staircase to access my portal.

FYI: you have to break most or all of the previous portal to get this to work.