I eventually solved the problem by hard-linking the files between my folder and the com.apple.BKAgentService folder, with the aid of some shell scripts to automate the process. Everything still seems to be working fine.
Doesn't look like there's a way to single out the Desktop via the 'Manage Storage' GUI.
However, you can always just symlink any directory from your iCloud drive; that way you can ensure that only the Desktop folder is being synced. This is with the caveat that while your Desktop files are being stored in iCloud, they're still taking up space on your HD before, during, and after sync. If you do it on every Mac then you'll keep your Desktop in sync between them all (files added, deleted, changed etc); this might not be what you're after though.
If symlinking isn't something you know how to do, instructions are below.
Backup (via TimeMachine or whatever you use).
Then fire up Terminal and run the following to move your Desktop folder into your iCloud Drive:
mv ~/Desktop /Users/<yourusername>/Library/Mobile\ Documents/com~apple~CloudDocs/
Then just symlink it to the usual 'Desktop' location:
ln -s /Users/<yourusername>/Library/Mobile\ Documents/com~apple~CloudDocs/Desktop /Users/<yourusername>/Desktop
Now anything that you add to ~/Desktop (by dropping things onto your desktop etc) will actually be dropped into your iCloud drive. They are of course still taking up local space on your machine. When you delete something from your desktop then it's gone from the 'Cloud' as well. The benefits of this are more for sync between machines (+ access via your iPhone of course).
If you've got another mac, move anything you value from it's desktop folder into your iCloud Drive 'Desktop' folder first, then delete ~/Desktop on that machine and symlink again as above.
Best Answer
Summing up the answer in advance: the folder simply might not exist on Windows.
And the workaround in advance:
If I cannot locate the folder, the only solution is via extraction from the iTunes backup, see: https://stackoverflow.com/questions/62434692/iphone-move-in-one-go-all-pdfs-generated-from-safari-page-prints-which-i-fr/62701384#62701384
I found a description that explains the equivalent Windows and Mac folders at https://deciphertools.com/blog/how-to-backup-ibooks-pdfs/.
Then there comes an explanation of how to use iBooks for iCloud, but only on Mac:
The checkbox "iBooks" does not exist in my iCloud > iCloud Drive settings. This could mean that it is simply not possible to sync iBooks with iCloud on Windows, as @MatthewBarclay commented above. This is also plausible, because my iBooks are backed up, and Apple does only one thing of the both, either sync or backup. And then, to answer the question, there simply is no such folder.
I have also tried opening it in terminal, as it could be hidden like the answer stated at Locating the iBooks folder in iCloud Drive, and I could not find it:
C:\Users\USER\Music\iTunes\iTunes Media>dir /a
does not have it, showing both hidden and unhidden items with /a (for /a see https://www.computerhope.com/issues/ch001039.htm).
Perhaps my sync settings are corrupt or wrong. Because I marked iBooks to be included in iCloud, but they are in my iTunes backup instead (proven), and they can only be in the backup OR in the iCloud (not in both, thus, they seem to be ONLY in the backup), if I am not mistaken. Settings > scroll down to Books > iCloud Drive is switched on, that cannot be the issue, following https://www.topmobiletech.com/how-to-sync-ibooks-to-all-your-ios-devices/. I will not test this anymore, please test yourself and set a different answer which I will accept in case you find more.
If I cannot locate the folder, the only solution is via extraction from the iTunes backup, see: https://stackoverflow.com/questions/62434692/iphone-move-in-one-go-all-pdfs-generated-from-safari-page-prints-which-i-fr/62701384#62701384