@ Hlitner thanks for your feedback. My question was actually prompted by our recent experience on a Westerdam cruise from Yokohama to Taiwan. The last Japanese port before Taiwan was Ishigaki but because it is only a small island, Japanese exit procedures were done a day earlier in the larger port of Naha, Okinawa.
It’s hard to make plans for ports, especially any private tours, without knowing where or when we need to clear immigration control.