I think the act of flipping between them is not meant to be a common event. But I do agree they do need to clean up the edges, although I don't think its "critical" for v1 of Metro.
I do agree that cohesiveness is important to the user experience. It makes me a little disappointed that the extra step wasn't taken to make the Metro UI live on its own without the full desktop experience tagging along.
To put it another way, I'd much rather have bumpiness shipped on day X rather than a delay to clear up all the transition bumpiness and ship 6 months after X. Although I'd like to see updates that fix the transitions come out a 8-12 months after release.
What would make me very pleased is if they delayed 6 months to get it right rather than rush it out.