when i edit Favorites, I only see one item to delete. But there are many more items in Favorites.
Opus and Windows favorites are two different things. They look pretty similar in the folder tree. Are you confusing them?
Very likely because I've never seen "Favorites" in win10 File Explorer tree, only Quick Access. I did just google for Favorites and then looked in my users subfolder for Favorites subfolder. There was one but only had a few items, none of the ones showing in OD tree. Looked at Favorites under Default user and All users. Mostly empty.
But when i first click on the DO favorites asterisk, I see all the same items that are in the Favorites tree. It's when I select "edit" Favorites that I only see one or two of those items.
Most of those are Smart Favorites, not normal favorites I think (based on the separating line in the dropdown list of your second screenshot).
In other words, DOpus has added them as you regularly visit those locations. They are not favorites you have manually added.
You can prevent Smart Favorites from showing in the tree by turning them off in: Preferences / Folder Tree / Contents.
You can configure Smart Favorites in: Preferences / Favorites & Recent / SmartFavorites.
Good they were Smart Favorites. I turned those off.