And RTD has said in press statements about the upcoming fourth series of Torchwood that it's set in a world where everyone has known about aliens for some time, but that doesn't mean they aren't surprised when they appear or attack.
Sci, you're thinking as a fan, not as a television producer. As a fan, you
want things to fit. That's natural; it's the fannish instinct. But RTD and Moffat are television producers, and their duty
isn't to make things fit. It's to make the best damn stories they can make, and it's to get the biggest audience they possibly can. If Moffat believes that he gets the best possible
Who by being consistent with RTD's
Torchwood and
SJA, then he'll be consistent with those shows. If RTD believes he can get the best possible
Torchwood by being consistent with Moffat's
Who, then that's what he'll do. But if
either believes that the best thing for their show is to ignore the other, then that's what will happen. There's no reason that
Who and
Torchwood must absolutely positively be consistent with one another. Creativity and ratings are going to trump consistency.