No, they really aren't. If a site opens a .swf file in a new window, Chrome should behave exactly as though it opened an HTML page that embedded the SWF, i.e. letting me approve it, and playing it if I've whitelisted the domain. Instead it will always download the SWF if you have your Flash content settings set to anything else besides Run Always. It's really stupid and it means I have to keep Flash enabled globally (which I really don't want to do) simply because Google doesn't care enough to handle edge cases properly.