Philip Padgett's apartment was the same set as Mulder's apartment - just without the furniture.
John Hawkes had actually auditioned for the part of Pinker Rawls in the previous episode, Trevor (1999). Although he didn't land the role, he made a suitable impression on the production team that they wrote the part of Philip Padgett specifically for him. Hawkes had always been on the The X-Files (1993)' radar, having auditioned for Eugene Victor Tooms back in Season 1.
With the production's move to Los Angeles at the start of Season 6, budgets had soared for the show. This was a conscious effort on the part of the writers to come up with a simple story that involved existing sets.
As Chris Carter was busy penning the pilot script for his new series Harsh Realm (1999), John Shiban and Frank Spotnitz mapped out the story before handing it over to Carter to finish off. Carter added in the writer's infatuation with Scully, something he himself could identify with, given how the character had grown over the years.