I think that's a valid point, but I'd like to introduce a few reasons why google may see them differently. Adobe has developed a sandbox for flash, adobe has been working with google to leverage the chrome sandbox (at least in windows), and adobe has given google access to early builds and authorization to distribute them and keep them up to date, so that google can know that if they're running flash it's not an out of date version. In several cases google has been shipping flash security updates to all chrome users before adobe actually pushed to their installed base (which only checks for updates once a week and needs the user to approve them). In comparison, quicktime security features and update practices are considerably worse off.

I think the word that java is also disabled in the nightlies in the same fashion should suggest that this isn't some partisan x264 or open web fight. It's security.