Apart from l*y lines, or the involvement of ETs, I can only think of one reason why anyone would want to create a "hidden" alignment, and that's to produce a straight trackway between monuments.

Or maybe hidden alignments just grew up naturally - local people would get to know the shortest route over a hill from A to B, and when C came to be built they stuck it on that well-worn track. A sort of motorway service station effect.