Time flows differently there. She can pop into a section where time flows more quickly and pop out weeks later having actually spent only hours, or vice versa. The timing of her pregnancy was completely within her control. I mean, if she was 200 years from the next starborn cycle, then she probably couldn't have done it, but having her pregnancy last 1 week or 3 years in actual time so that she could line up with the astral event was almost certainly doable for her. And we have this from Morgan's Journal in his microfiction:

The thought of allowing a Destroyer to be birthed among us when I could have stopped it is too heavy to bear..

This is him worrying about his role in letting Margaret give birth to a starborn that may be evil. How could he have stopped it? Several ways, I suppose, but only if he knew it was coming. So he knows, and somehow she doesn't?

The pregnancy could be a happy accident, but unless you're claiming that Margaret didn't know how to make sure her child was a starborn, then she had to have chosen to do so. Even deciding to have Harry per the natural schedule is a choice. Can't be an accident unless she's ignorant of the whole thing. Maybe she was, but it seems really unlikely to me.

I've got a problem with the rarity of starborn, anyway. Any kind of convergence that gets Harry and Listen probably gets way too many people. My headcanon (despite what Butcher seems to say) is that there has to be time (and maybe place) plus an intentional ritual at the birth.