So just what are runes good for? Besides that vending machine puzzle and nerfing transmutationer? Because it's so much fun to transmute three gems into three runes of false hope and then into another three runes. As far as the vending machine puzzle goes, if we read "rune of pillars" as an I, "rune of growth and decay" as an L, and "rune of scrutiny" as an O, the combination for the crafting machine is LIO, for booze, OLI; for food I think it's ILO; for thrown weapons I think it's OIL, and I don't know the combination for the bolts machine.
I never used Tranmutation, so I can't say why that would be a nerf, but yes, the runes seem only to be used for the vending machine spawn.