The Cables and Pipes in Mekanism don't make a Occlusion Test so they ignore if there is a multipart that blocks the connection.

EDIT: In this case the stone cover is made with Chisels & Bits

Mekanism does not currently have Chisel & Bits compatibility.

Thats a thing thats build into MCMultiparts. There is a class called OcclusionHelper and this class has a method called occlusionTest or slotOcclusionTest. This Methods check if the cable collides with any other multiparts.