I'm thinking of adding the user interface for this new feature to the Collection document's tab
Settings >
Sorting, like this:

Say that our Collection document is set to “Sort alpha-numerically by Name” (the default setting) and a certain parent folder has the following arragement of 3 folders and 3 bookmarks with the following names:
A Folder
Some Bookmark
Another Bookmark
Nice Bookmark
Another Folder
Some Folder
Referring to the screenshot above, let's say you bulleted “Folders over Bookmarks” and switched on “Sort folders only”, then clicked in the menu: Bookmarks > Sort all (or sorting is done automatically, during a syncing operation). The result would be that the parent folder described above would be rearranged to look like this:
A Folder
Another Folder
Some Folder
Some Bookmark
Another Bookmark
Nice Bookmark
Importantly, note that, like the existing
Bookmarks above folders and vice versa settings, there is only one
Sort folders/bookmarks only setting which will apply to all folders in the whole Collection document. That is, you could not have different settings per folder. This is in the interest of keeping things as simple as possible, which is best for developers and best for user.
What do you think?