Chris86, Apparently they were using the wrong stones as it does take different stone materials and grits for aluminum, cast iron and Nikasil. Using the wrong stones will definitely mess things up and as well as previous mention running hone too higher of a rpm will also gall the aluminum cylinders.
Even if the cylinder is bored it still got to be honed to produce the appropriate 45 degree cross hatching.
These guys are probably the same guys that say you can't hone 2 cycle cylinders because they don't know they got use ball type flex hones because regular flex hones catches on the ports. Yes some cylinders can't be honed or bored due to ultra thin chrome or Nikasil coatings and the honing ears right through that coatings. The problem is that equipment like chainsaws and trimmers is even if you hone to remove the scoring oversize pistons and rings are not available so there is no point in doing it. Now larger 2 cycle engines which I have not worked on may have OS pistons and rings available.