Now I've been a consumer and producer of crossover fanfiction for thirty years. I think I have enough perspective to know when consistency is important and when it isn't. If Venus Flytrap has two backstories, and DOCTOR WHO has three different histories of Atlantis, and every hero knows someone who was really Merlin (or, in the Doctor's case, will be Merlin), then I'm not going to sweat having Clark Kent less than six degrees of separation from Dana Scully.
This is just the wrong website for people who are bothered by things like that. Sorry.
(It may be of interest that there's a cartoon in the archives which establishes that it's not DOCTOR WHO that Andrew has seen all of in Smashed.
(If you really, really can't live without some sort of explanation for the Scully-Kent paradox, see this cartoon for another situation whose rationale could be extrapolated to apply here too.)
If you didn't understand why Giles might find Lois & Clark's baby familiar-looking, you haven't read One Child Born and Posterity on my fanfiction index. You see, in Strange Visitor Giles is recognizing the child's family resemblance to ... but that would be telling.
Finally, Last Son of Krypton is a series of comic strips that illuminate the Doctor's lifelong relationship with Superman.