There must be another place where the template for bookmarks is located otherwise you'll have to manually change it every time you've made a bookmark.
I haven't tried changing one yet but i predict it will stay the shape it is now, no matter what .png you replace a bookmark with in that folder, atleast that was how it worked on the N900 afair.
As the OP wants to change the shape I think he needs to find that template/mask aswell.

Regards Dousan...

e: just changed a bookmark icon with a custom .png (same size/shape as the org. bookmark .png. It changed the bookmark icon on the homescreen but didn't change the thumpnail in /home/user/.grob/I.