I picture the NRS team is divided on this subject and that's why it's not entirely clear what's happening or what they're going to do with it. The variations for MK just started in the last game, MKX. I'm sure it might have been an internal battle at first just to introduce that, it's a HUGE change to just have 20-30 vanilla template characters where the MU's are set in stone from launch. (before patches obviously)
So in my mind, I see meetings at a big round table where they talk about this... maybe even vote on it. I bet a few core members are voting against it because they feel like it would bastardize MK in general. That it would stray too far away from source material and more structured match ups.
The problem is, our community has made a pretty convincing argument. I originally didn't want it to change, then I didn't care, now I feel like it's stupid not to have customs allowed. How many abilities and combinations are being snuffed out for no reason? The answer: a LOT.
Hail to the fans. We pay your salaries and we love your games. Please listen to us. (not about everything lol)