This mod works great, even with Cubic Chunks mod (a mod that pretty much removes the world height limitation - both ways) - as long as the player is above y=0.
I know its a niche problem really, not many people use it currently.
But could you maybe create an option that is able to show caves below y=0 on map?
Currently it seems like you find the stuff to show on map by searching down from the players y down to 0.
A possible option would be a setting that instead searches down by a fixed distance (256 blocks for example) instead, and thus be able to detect caves below y=0 too.
Of course, if you handle the mapping different that doesn't apply.
I understand if it's too much work for a too small target group, but if it's not hard to implement, such an option would be nice