Not "our son" that left "us both" with "an emptiness that can't be filled," ala I Want to Believe. Not "my son" and "his mother", ala The Truth. Not "That doesn't make him any less of a miracle though, does it?", ala Existence.

Mulder is mainly granted snippets of fatherly recognition via his role as an auxiliary attache to Scully's arc. Although Maggie mentions Mulder's son on her deathbed, Home Again focuses primarily on Scully's loss. Regardless, My Struggle III casts doubt on Jackson's paternity soon thereafter. Even when Ghouli attempts to patch up a few holes-- e.g. Wong crafting a scene to underscore internalized pain and shame:

The moment it felt like Mulder was able to express his grief was when he and Skinner were talking on the boat. The moment I really love is Skinner is warning him to stay away, and Mulder is like, ‘Thanks for the warning, but you’re too late.’ The moment he turns around, we saw him not saying that to Skinner, but saying that to himself. The whole thing was too late for him. So that’s the moment I liked.

--Mulder is still left outside the sacred circle (i.e. a scene explicitly exploring his parental grief), bearing witness to Scully's loss in the morgue without being able to express his own. My Struggle IV then knocks away any future examination by doubling down on My Struggle III's revelation, severing the Mulder men's connection entirely. He's allowed one smothering hug before Jackson distances himself and fakes his death, before Scully tells her partner to write off the child he's loved as his own for nearly eighteen years.

Because William-Jackson doesn't consider him a father.

Because Mulder's just there to support Scully.

As tempered as I attempt to be concerning the Revival, My Struggle IV's insistence on creating more mystery rather than answering old questions added (likely unintended) insult to injury--

March 21, 2018:

[Interviewer]: If the show returns and if Gillian returns as Scully, will Scully still be able to sense that William is alive? Or has that connection somehow been severed? [Chris Carter]: Because he’s still alive, there is that connection. I imagine right now, that’s what she sensed at the end of the dock at the sugar factory: William might in fact not be dead.

If that be the case, canon would be justifying Scully's lie by omission: that she'd directly or indirectly deceive her partner of twenty-five years in order to nudge him to "let go" of Jackson (which would, in effect, taint her characterization.) Why?

Because the William arc isn't really about Mulder, you see-- he's an accessory to Scully's bond with William. The shoulder to cry on, the unfailingly supportive-- but passive-- man who lets her adopt William out and lives with her through the pain and waits for her after she leaves and reopens the files after she brings a case to his doorstep and agrees when she insists they find William before the world ends and caves when she asserts they stop looking-- and give Jackson up-- because their son, their baby boy, is "an experiment."

Because Mulder "can only connect" to his personal journey of fatherhood "through her."