I could see bookmark management under Preferences, sure.
I just don't logically see bookmarks and extensions together by themselves, they are just different things. But you could group them together if there was others stuff in the group as well. Basically anything the user is going to want to 'edit'. Things like UI settings, download locations, search engine defaults, etc you can put bookmarks and extensions in that group as well. I just don't see them living together as a separate group. they can be apart and each have their own setting but they don't make a very good group, IMO.
I'm not sure I am explaining this well.
I think Extensions having their own menu is fine. And now that I know they have their own menu I know where to look. (No idea why I didn't see it earlier) AND given the importance extensions have in a modern browser it is totally appropriate for them to have their own menu. However, I do worry about too many menus. The (very) old school designer in me says you should try to stay between 7 and 9. Some of those are system menus I know but Orion currently shows 11 menus in my menu bar. IMO that a few too many.
So what is the answer? <shrug> Someone will have to make a choice, and be able to defend that choice against people who come later and say 'Thats wrong, do it this way' Because the last thing you want to do is constantly change the experience for the user because no one know for sure where it should go.