If you flag a comment for a post with score of at least −3, for example this one (the links is for Stack Overflow's 10k users), the dialog box will appear as in the following screenshot.
It would be preferable not to change the transparency of the dialog box, as it doesn't have any purpose. I don't need to be reminded I am flagging a comment for a post with a low score; that is already evident by looking at the post itself.
The screenshot has been taken on Safari 5.1.7, but I get a similar effect on Google Chrome 20.0.1132.57, and Firefox 14. (I know, Firefox 14 is a beta version.)
As side note, the editor buttons cover the dialog box, in the last two screenshots.