When both this mod and the Janus planet mod (https://mods.factorio.com/mod/janus) are enabled, pipes are no longer able to cross over/under each other.

What other mods do you have installed?

With this modlist, you cannot build on top of underground pipes (with some exceptions like elevated rails):

{
  PlanetsLib = "1.2.12",
  base = "2.0.32",
  ["elevated-rails"] = "2.0.32",
  janus = "1.1.1",
  quality = "2.0.32",
  ["space-age"] = "2.0.32",
  ["the-one-mod-with-underground-bits"] = "0.1.4"
}

Interesting. I'll look into it.

Fixed for next release