Cobalt is dime a dozen. It doesn't make sense that some guy who botted his crafts to 50 can make the best gear in the game while those who actually put the effort and teamwork into clearing difficult raid content get useless chaff. Until you can make a bot run Darkhold and Ifrit, crafted items that don't have NM drops as components shouldn't be as good.

Also, you can't really mix the R/E gear with the forbidden materia system. Even if you didn't have to trade to add materia, R/E gear is so much harder to get (and you can only have one at a time) than a generic high level crafted item that it'd be terrible to have it repeatedly blow up. Being able to turn R/E gear into special materia is equally a bad idea precisely because the farming that special materia would be a never ending grind.