What's in question is whether the book's version of the Prime continuity is consistent with later canon, because if it were, then DM's MU could just be treated as a different alternate timeline.
Surely it doesn't matter how consistent the book is - it's always an alternate timeline? Its version of the regular universe may also be alternate, but hey, them's the breaks.
Besides, it could be argued that if the book's MU is alternate, then it's more likely its RU is also, because it may be just easier to cross over. Meaning: The novel's versions of the RU and MU may just be connected in some way, rather like the canon versions of same. This would explain why it's so easy to move between them.