It is weird, because it works completely differently from how it works on the ground.
It's likely this way so moves like Sindel's air scream or Kitana's air fans work at all.
As a side effect, it also enables you to do predictive anti-air jumps that you cancel into an attack if the opponent didn't jump (Kabal).
And lets you tuck in your toes for someone who otherwise leaves them hanging (Kotal j2 xx air kat).
It IS obnoxious though. As bad as anti airs are in this game, when you finally download some one and try to anti air them, they cancel into air specials late as hell and you get bopped. It feels like bad design.
It is janky but this is something that's ended up being really cool in some cases in the past few games. Injustice 2 had a few characters with air movement like Brainiac who would throw out these really huge jump normals that he could cancel into divekicks or swing around with his tentacles. Actually made for some fun gameplay. ;Maybe D'vorah or Sindel get some mileage out of it in MK11.
But on the idea of anti-airs getting messed up by air attacks.. that's really just part of what makes that shit good. Like Kabal's downward air saw and Jade's downward air glaive, it's a big deal for those moves to be able to change the jump arc and mess with your anti-airs.
I know people would probably like to see more consistent anti-airs in this game but I do think they want jump attacks to be strong(maybe not every character) with mindgames like this.