For me, if buses run on a mostly reserved basis and I have a reservation during high season, I'd want to show up a bit early to make sure my reserved spot isn't given away. If it were fully reserved then yes, I would probably time it a bit closer but still leave some time to use the restroom and grab hydration/snack.

I know most repeat Japan visitors expect Japan transit to run like clockwork. Big city transit systems mostly do in decent weather conditions. Popular tourist attractions can be a scrum in their own ways. I think it is reasonable consideration to ask if Kamikochi's shuttle system is holding up these days given the popularity. I hadn't thought of how crowded Hakone gets during a 2025 visit and should have changed my plans to depart earlier or later than check-out via the train rather than waiting for the bus after it snowed & I wasn't near the start of the bus line. Saw some people who couldn't board. Live and learn.