SilverHeart

Ah yes, I was wrong. That's just a cameo appearance. It's a very very minor part of the story. He never interacts with Littlepip or has an effect on the main story other than Homage talking about what her former marefriend told her. It's just a passing reference for Dr. Who fans. She did that with a few different franchises and stories.

Well, that sort of opens up a plothole(no pun intended)

Well at least from my PoV

Not really, I'm no whovian but doesn't the Doctor only interfere when time isn't flowing accordingly? As in someone is trying to do something that isn't supposed to happen? So if he didn't show up that means time was fine. Regardless, it really has nothing to do with the story. It was just a fun little nod to Whovians.