>>42533272
It's all but confirmed by Where the Apple Lies.
Granny Smith says "the whole family" was at the hospital, and that's Granny, AJ and Mac, no Pear Butter, Bright Mac, or Apple Bloom. That means it's after AJ & Mac's parents died, but before AB was born. Ergo, Apple Bloom's parents had to be someone other than Applejack's parents.
You can make all sorts of excuses, from "LATE SEASON!!!1! NOT CANNNON!!" to "Granny is an unreliable narrator" to "the writers are a bunch of queers who don't know how reproduction works, and think a baby is something you just pick up at an orphanage and dispose of after the ritual", but this is the story I find works best. It adds to the theory that the mane 6's elements are the virtue they need to work on the most.