One technique is to use the #anchor tags which can be interpreted to go to a specific scene, and change when the scene changes for bookmarking. The code to do this is shown in this post:
This is probably the best way given your requirements. Because it still is on the same page, image preloading and such will work to reduce flashing (although depending on your content, a browser may still need to do a lot of work to render the scene).
Does that solve it for you?
P.S. this technique was recently used in this post, using a single scene but to allow individual within to be bookmarked.