Ok, this is not the best fixes for the issue, but is not too awful...
I don't tend to use bookmark folders, but made one last night for all future bookmarks that I do not wish to have in my Favourites. Scrolling to get to it and then scrolling within would be annoying but never mind.
Apple's official support pages suggested opening the bookmark sidebar, and dragging in new bookmarks. It works fine, but doesn't especially suit me. What I did notice though, was that the bookmark I dragged in as a test did not go to the end of the list of bookmarks, but stayed where I dropped it...
I scrolled down to the bookmark folder I had made the night before, and dragged it up to the top of the bookmarks. Yay! It now appears as an option in the traditional place, and no scrolling required. One can place folders within that folder, and these nested folders appear in "Add bookmark..." also.