Just try looking at that and saying otherwise! Oh... you mean biologically? Well, I'm not sure why this was still a big question two years after Baby Cakes, but answer away!

Edit (14/5/22): Just realised I forgot to post my actual answer before.

Legally and publicly, yes. As for the biological details, he doesn't quite understand MAR* treatment well enough to say - he's just glad it worked.

*Magic Assisted Reproduction. Still in the early testing stages, and even if the Cakes hadn't signed confidentiality agreements, you just don't talk about this kind of thing to acquaintances in a maternity ward. Pinkie may know, but if so she's Promised not to tell.

28. Is Mr. Cake the father of the Cake twins or not?
Yes.

Yes, he is. We got the gag at the start of Baby Cakes because it does look strange for both of their twins to be different races than both parents, but it's just a statistical anomaly.

LOL, No! Both of the Cakes are infertile, that's why they adopted Pinkie Pie, but after Celestia came into town to their shop, they figured they would ask a favor, so in response, Celestia grew a dick, fucked them silly, and left one hell of a “gotcha”. They now both regularly attend Celestia's Pleasure Parties.

7039473

--Sweetie Belle

7045615
Hmm... so by this theory, pegasi or unicorns couldn't have earthpony foals?

7045641
Certainly seems like it, though I just noticed there was a revised version.

This theory's also from 2012, and predates Flurry Heart...

--Sweetie Belle

7045664
Hmm... very scientific, but I think I prefer the likelihood to be the same for each tribe per genetic contribution.

I really like these comics. The format is just hilarious, I love it.

As for my own thoughts... I think he's the father, yes. But considering this is a world full of magic, I'm not entirely sure I want to subscribe to, or even get into, the whole genetics discussion. There are literal magical forces at work, stamping ponies' flanks with cutie marks. (And quite possibly steering soon-to-be parents in the right direction when choosing a name.) I think things might be a tad difficult to understand for people not living in Equestria. Or this plane of existence, for that matter.

I don't really like to rely on the whole 'it's magic!'-explanation, since it's by nature more of an excuse than an explanation. But there are certain points where concessions have to be made. And 'it's magic' still sounds less annoying than 'I don't know'. (Which would be more honest, but hey.)

7030253 Yes. It's extremely rare, but children can obtain recessive genes from their parents that were long dormant in the family tree. Genetics can be full of surprises.