Eh, I don't like this part. It's makes runes depends on Some Guy/Gal from the Other Side, and this guy/gal also ex-dwarf.
Situation where grooves and stripes in stone (optionally filled some special material) just Do Things because this is how world works I likes much better.
Maybe combination of lines and ways actually can do something. Also can explain why some crystals, stones and metals more magic than others — maybe on microscopic level their structure replays some (probably unknown) runes (with proportionally reduced effects).
A thought aside: Has anyone tried planting cultures in the shape of some simple rune, say fertility? Soil, of course, is a less reliable material, but if it only has to last a year...