Something tells me that the extreme circumstances needed for both Rarity and AJ to remain alive alongside Twilight after she was made immortal was one of those “alteration of fate” sort of deals. Celestia wanted the Element of Magic to be an immortal alicorn even though it was always a package deal with the 6 main characters, and now the element of honesty and element of generosity are walking around willy-nilly 100 years later, and I wouldn’t be the least bit surprised if similar fates happened to the 3 remaining of the Mane 6.
 
In other words, if a reaper has been sent, the natural order of death in Equestria must be close to being completely fubar’ed.
 
In most stories where a reaper is dispatched to kill someone who should be dead, it usually means someone powerful messed with the natural order to suit their own desires.
 
(Me, I blame Celestia. Heck, even in the canon show her attempts at nepotism were absolutely ridiculous. It started with the first Sombra episode and just kept spinning out of control. The episode even implied that others like Luna were warning her against it but she was ignoring all opinions on it)
 
In other words, I doubt that Baphomet jr is a villain, just that the balance of death is a very low priority in Equestria, which is very concerning to other realms.

Even Baphy loves her mama!

Mission failed successfully.

Awww poor little thing.
 
I want to hug her to comfort her

Better luck next time