Currently you are able to build underground pipes anywhere in a Factorissimo factory building. It's not much of a problem for the factory wall tiles and entrance area, but being able to build underground pipes into the void is a bit egregious.
You also currently can't make an underground pipe connection into/out of a factory building. Factorissimo registers that there are pipes on each end of a connection point, but does not generate an underground linked pipe between them, though that's a relatively minor issue.