Yes, that is true. However, New Bark Town is the link between Johto and Kanto, and is basically in the southern part of Kanto. One would assume that the flooding continued to there. ^^
EDIT: OMG I TYPE TOO SLOW
Yes, but one would also assume they would put Johto and Kanto not just Kanto.
And I like the idea of flooding. You could also flood towns near water like Celadon City because it has water in it and on some of the routes around it. And some rivers going through the nation.