Typically, what gets stored includes what is normally in Documents and Desktop, particularly if "Optimize Storage" is also selected. From Apple:
Note the section about "An app" at the bottom. If Safari is selected, bookmarks will be stored on iCloud Drive.
@rbpeirce says that iCloud.com shows almost 3000 items, so somewhere Safari has been selected to be on iCloud Drive. To be shared, I think what one would do is to turn on iCloud Drive, then select Settings>iCloud>Show More Apps> and toggle on Safari. I suspect that if one syncs Safari through iCloud AND turns on iCloud Drive, the bookmarks end up stored in iCloud.com as
@rbpeirce is seeing. As I said before, I don't use iCloud Drive, so I cannot verify that myself, but I do know that with iCloud Drive OFF and Safari set to sync through iCloud, bookmarks sync just fine between my iPhone and Mac, complete with folders. So, right now, the only known difference between his
@rbpeirce's system and mine is that he is using iCloud Drive and I am not.