According to the tour description of the included shuttle "the coach will drop you off at City Hall" and goes on to say "after 6 hours of free time, reboard the coach at the drop-off point (City Hall) and return to the ship."
Another option is the Silversea "included shuttle" from the port to central Kyoto. They say it's only 1 hour but I'll bet it's more like 75 minutes. Just don't miss the return shuttle unless the ship is overnight in Incheon.
We used Stugeron 15 for our Antarctic cruise on the Venture in 2023. Tried it at home to make sure we had no bad ill effects. Had no problems. On both our crossings we had the "Drake Quake." 12 to13 meter seas. We never got ill and felt the Stugeron was great.
Bingendore we are doing essentially the same thing very soon but only 2 of us. We’re using Chris Rowthorn Tours. We have a guide meeting us at the Osaka cruise terminal to escort us to the high speed train to Kyoto. Then another guide meets us in Kyoto and we spend the day touring in Kyoto and then make the return to Osaka the same way with the guide in Osaka escorting us back to the cruise terminal.
I'm pretty sure if you go on the Tours by Locals website you will find what you are looking for for each of the cities you list in the Asia board.. Here's an example for Kagoshima.
https://www.toursbylocals.com/KagoshimaLocalExperienceTour