he's wrong, the reason he could annex the other one was because he had surrounded it with his land, meaning daimyo's with their capital non coastal can be annexed
He just needs to find a way to get rid of the green one and the shogunate will actually disband then
That was moving the capital, not eliminating it, I think? I'm just extrapolating from what I know of game mechanics and from what Prawnstar himself did earlier in the AAR - he took Liguria off Genoa and thus eliminated them in a war with their Milanese overlords. Japan is something weird, though, and I might very well be wrong.