Personally speaking no, unless someone optimizes it and does a run that is on par with recent runs ? maybe
Just because it doesn't exist doesn't mean it should be there when no one does it like the segmented category. Restricting Transmutation Runes doesn't change much like you said fights will take longer. It also doesn't help that the run has forced sections we can't skip and QTEs..etc.
If there was demand. I suppose we could. That being said, the DLC is pretty cheap, and goes on sale pretty frequently. We have the modifier for the runs already on the board, so people running without the rune already have a place to submit, they're just competing with people who have the rune.
The other thing to consider is, whether people actually want to run the category. I don't think any of the runners on the board right now would want to do the run, since it only makes you have to either get magic, or farm for relic drops/ go to the store a few more times. It doesn't really add any skill to the game, just RNG/ farming. If more runners pop up and really want the boards to be separate, that's fine.
Basically what Church said. I think I was the person who initially pitched using DLC to circumvent the more annoying parts of the run. If you want something a bit more robust, take a look at the NG runs. There is still plenty of optimization to be had across the board in this game; I just have had other gaming/running priorities.