I’ve spoken with @mano-wii, it seems the current limitations are known and they will be solved, also another tool is under development that will allow for full tunnelling it seems, and it may fully replace the current manifold extrude tool:
⚓ T75913 New tool to add and subtract prismatic volumes
I hope the limitations of the current manifold extrude tool are solved rather sooner than later because IMHO as it is right now it’s usefulness is pretty low I’m afraid, it’s basically like detaching the faces and moving them, but you cannot past the first edge, it won’t be destroyed 