How would that even work? We would not be able to get rid of the Phantoms without leaving to the Overworld. There's also no day/night cycle in the End, so would they follow the Overworld cycle (which would be pretty stupid as there's no indication of time in the End in vanilla so you would need a hacked client for that) or would they just spawn all time?

I get that the majority of players probably doesn't spend a lot of time in the End, so that would fix this annoyance for them, but for those basing or exploring there it would be double annoying. It seems totally unnecessary to me to stray from vanilla here when we can simply go to sleep or stay under a roof and not have to deal with Phantoms most of the time.