You’re probably wondering why is it that Petunia doesn’t resemble Bulk at all. The truth is: he’s not her (biological) father.
Petunia was conceived at a rather conflicting night. Bulk and Fluttershy work pretty well together, and they almost never argue. If they do, it might be about something frivolous. That night, they had the very first and most terrible argument anypony has ever seen. You could hear sounds of breaking furniture if you were around. Fluttershy eventually left home and spent the rest of the night in a bar. Or at least, that was what she intended to do. She’s never been much of a drinker but that night she got pretty drunk and accidentaly had something like a one night stand thing with a fellow stallion. Fluttershy was so drunk that she probably thought it was Bulk but, who knows.
Eventually she sorted things out with Bulk and when they found out she was pregnant, Bulk forgave her and decided he’d adopt the child as his own. Btw, Fluttershy just couldn’t forgive herself. She went through a tough and depressive pregnancy, but she though it was all worth it when she saw Petunia for the first time. She was Fluttershy and Bulk’s little bundle of joy and the apple of their eyes.
As for the stallion, Fluttershy never saw him again.