Dinky and Sparkler aren't their biological kids, They were created via genetic loom( like Jenny in " the Doctor's Daughter") on one of Doctor and Derpy's adventures, maybe the same thing happened to the Doctor and created Doctor jr. I don't really see Doctor and Derpy making whoopee, so I'll stick with that explanation.
THIS is the direction I wish they'd taken the TARDIS in. It's become so sterile and lifeless. I love how the floor almost looks like a stained glass window, and how full the scene feels. It may have taken the better part of a thousand years, but he's finally got enough people to pilot her correctly.