I've been using Mail.app with Gmail since DP1 with four separate accounts and your experiences are exactly the same as mine: business as usual except for the hundreds of draft messages being generated due to "Store draft messages on the server" being re-checked.

I do, however, use smart mailboxes: they have no effect on the functioning of Gmail. They shouldn't, either: they're not much more than local saved searches.

I suspect this might be a case of correlation rather than causation.