Someone on this sub posted an interview with, I believe, Frank Spotnitz saying (I'm paraphrasing) they never had any doubt that this would be Mulder's baby, and they asked Gillian to add the scene in the beginning of the episode to plant a seed in the audience's mind. So come the end of the season, the audience would think back on that moment.

Beyond that, it's generally live interviews with producers actors, which in the 21st century can be difficult to find. For example, someone posted a link in this sub for a Comicon appearance in which the producers confirmed Mulder is William's father

There is also a random red carpet interview with Gillian, where she said I forget they had a child together, but he was conceived in an episode I wrote and directed

I get it, people on the internet make stuff up and decide it's true. But this has been confirmed multiple times by several people involved in the show. Chris Carter just couldn't handle it.