Hey thanks. I was looking at the same issues. Your workaround works for me. You can pass mostly the same args to get_bookmarks() too, but if you can ever figure out how to do it with wp_list_bookmarks() let us know. I’m still playing around with it myself.
As far as having 2 default categories, I noticed that too. Under options you can now set a default post cat and a default bookmark cat (or I guess they could be the same). So it looks like this is perfectly ok, although it would have been nice if it said ‘Default Bookmark’ or something like that.