The change in materials on runic hammers. This is just my thoughts without doing research on the topic, but I believe that the higher quality of runic hammer you use will.
1) Stats on wep will be higer, example being if the toxic got you hitfireball 35, plat will be able to get you hitfireball 45. Not exactly 10 higher, but there will be a difference.
2) More stats added. From my experience using a plat hammer adds more stats to weps than other runic hammers.
I would suggest just using plat runic hammers, it's the only form of hammer I will use when crafting.