I agree that if rare items were able to have runewords made in them that the current upgraded version of the runewords would probably have to be reverted back to the originals. I'm leaning more towards thinking Game wouldn't like this idea though.
He's said to me several times that he doesn't like runewords being the best endgame items. One reason for that is because their easier to make/get compared to the custom items. Still everyone can hope wish and dream, it never hurts to wonder.
Edit: Also not only runewords but rare items themselves might have to be changed if this was to be added. And since I think all rare items I believe? we're just buffed recently I doubt Game would wanna lower them just for this.