See also: Sweetie Belle is clearly Rarity’s foal. Everypony pretends they are sisters to be polite.

1. “Even littler than y’all” and “When [Applejack] was your age” sound like exaggerations/approximations. We’re treating flashbacks as suspect but taking dialog at face?  
2. Granny looks younger in “Apple Lies” despite using her older design in “Chronicles”. That suggest the parents weren’t there because they didn’t have character models as they were unimportant at the time. They could have been busy with Apple Bloom at the time/said goodbye offscreen.  
3. Jim Miller stated they were “away on a couple’s vacation.” >>1366756 They likely took Apple Bloom with them given how young she’d be. “Whole Family” refers to the remaining members at the farm. And Granny was the owner and matriarch of the farm, hence why the were trying to convince her not their parents. And Diamond being (secretly) born prior would explain why Filthy married Spoiled despite her character, and what the show would do over Apple Bloom being the product of incest if it had to choose between the two.  
4. If the “Going to Seed” flashback was meant to be unreliable, why even have it? If it wasn’t supposed to be taken semi-seriously, why would it be important enough to the story to even include?
    
   Most likely they meant to retcon Apple Bloom’s age no matter how much it contradicted prior works. Maybe the unreliability of the flashback was meant so those inclined could ignore it they felt it made no sense.

I think more about maturity level more than literally age. I think of them from anywhere from 12 - 17. I use the excuse that horses age differently than humans to give them their adult independence.