Not at all what they said in the press release. The quote is "The game follows a plot that runs in parallel with the established 5th edition storylines, but does not cross over directly..."
That does not make it "explicitly separate," all that means is they are not going to shoehorn in whatever villain and plot are in the next book. Doesn't mean they cannot operate in the same space, and the implication that the game runs parallel seems to indicate they will occassionally take place in the same places. Nothing here disporves the assumption that Waterdeep and Undermountain are next, and I still believe that come June that will be the products announced.