Chris Carter himself admitted this episode wasn't necessarily the "return" of Mulder, nor would it completely explain his absence - if it did, why would we watch any more? I think it's Fox that's trying to over-hype each and every episode now, not necessarily the show's creators.
Duchovny will be back full-time for 8 episodes this season (he did cameos for another 5, some of which have already aired), and he's said he'll do another X-Files movie and is "open" to appearing as a guest star in another season of the show.
I'm still halfway through the episode, so I don't even know how it's going to end yet, but I assume by jacobnero's post that they don't find Mulder yet.