To be searchable in Rune Trader by faction? Right now I find it hard to find the right faction without guesswork Maybe I'm missing something?
I will say, that in the beginning, I'm fairly confident they weren't designed/planned to be traded =P. Though for the trading, you do bring up a valid point in terms of same name runes.
Right now the best you can do (iirc) is match the order of the rune checklist with the rune trader dropdown list.