What’s wrong with using the Runes to empower the paper, much like it is used to empower a body? Runes are like Magic Crests, so in turn you are giving the paper a pseudo Magic Crest. From that point, the paper is part of the materials for whatever alchemic procedure he is conducting, add the ink to the paper and there are more materials. Heck I think I just described a stamp, slap that on something and boom, you have fire or whatever the rune does. Add that to whatever spell you just wrote up and you can have a chain reaction. I'm aware it doesn't work like this, and that is taking some liberties, but hey, I think it can be interesting.

Leaving work rite now. I'll be back in a few hours.