While I agree they're not as important, the little bubble up in the corner is already hard enough to notice without it having to blend into the background. The color is much more noticeable on the beta theme where it stands out. It needs to be customized more on these sites where it's not noticeable.
Noticeability on sites where it blends into the background:
Compared to noticeability on sites where it contrasts the background:
As you can see, some sites have a very high contrast to the sky blue, which makes it stick out just as much as the red. Other sites, such as Stack Overflow and Pro Webmasters, do not, which can make it much harder to tell you even have a notification. Therefore, I conclude that the "this notification isn't as important" argument is invalid. It's clearly not as "hidden" on other sites. The sites where it's hard to see just need a slightly altered, more noticeable color, or a color that better contrasts throughout all the sites.