Thank you for providing more details. I have no objection to segregated tags on roads with white lines to separate cyclists and pedestrians.

There are two points. The first is that the tag cycleway is for separate paths, as stated in the documentation. Even in the shared path example you showed, the paths are separated. The path mapped as cycleway in this chnage is structurally part of the road and adjacent to the carriageway, so it should be sidewalk.
The second point is about the bicycle=designated designation. You quote the sentence ‘Cyclists should use the lanes marked for bicycles on sidewalks or roads when they are available’, which means exactly that: bicycle lanes on the roadway if they are on the roadway and bicycle lanes on the sidewalk if they are on the sidewalk. This does not alter the principle that cyclists should ride on the carriageway. It is also true that cyclists ride on the footpath on roads where the carriageway is dangerous, as https://wiki.openstreetmap.org/wiki/Tag:access%3Ddesignated says ‘Designation does not make any statement about whether the way is actually usable for the designated purpose.’ Also, the area with the bicycle symbol is called the ’普通自転車指定通行部分’, but this is still part of the footpath and pedestrians have priority. Please see https://www.keishicho.metro.tokyo.lg.jp/kotsu/jikoboshi/bicycle/menu/rule.html for details (sorry I couldn't find english resources, I hope auto-translation will help you).

Japanese traffic laws related to bicycles are so complicated that only a few avid cyclists can fully understand and obey. So some osm users in japan made up the guideline for tagging cycling infrastructure https://wiki.openstreetmap.org/wiki/JA:Tag:highway%3Dcycleway#%E6%97%A5%E6%9C%AC%E3%81%A7%E3%81%AE%E8%A7%A3%E9%87%88 so please read it through.

Anyway it's good to have this conversation with you and please let me know if you have further questions.