So it seems iBooks does sync bookmarks etc., for sideloaded non-drm epubs, via iCloud. If only Apple would come out with iBooks for Mac, then... problem solved. Why they don't have a Mac app, when all the other major platforms do, is a mystery. I suppose they sell more iPads that way. I for one will continue to get my purchased books from Amazon, since they sync between my MacBook Air, iPhone, and Kindle. I will also continue to complain that it's impossible to sync non-drm books between my MacBook and iPhone!
If there was, I'd ditch my Kindle for an iPad Mini in a minute...