How exactly does "manual cache" of data work?

Correct. The ground tiles are stored in the rolling cache when you fly over them.
These can also not be preloaded manually. This has been verified by often enough.
This is also what @kreativeslime wanted to tell you above.

If you create a manualcache.ccc, you can preload photogrammetry of specific cities.
If you don’t create one, the PG will be saved on the fly in rollingcache.ccc.

Which cities have photogrammetry, you can see here:

However, I cannot judge how complete the lists are. New cities are added with each World Update.
Try it out. Manually load the area of a city that definitely has PG in MSFS (London, New York etc) and manually load a city that definitely does not have PG.