There are still people hanging on to the theory that it’s not the Doctor’s TARDIS… (or at least not the Doctor). So maybe?
Or could it simply be that the Utopia doesn’t follow on from The End of Days and we’re somewhere else in Jack’s timeline? (Negating everything I’ve said above).
Either seems a bit unnecessarily complicated now, and the latter is rather undermined by the Doctor’s “the rift has been active” – the most blatent Torchwood continuity line. I think what you see is what you get – and therefore, either they blew it, or it’s left to the viewer to make it work.