There is no (official) way to do this and I believe that it's like that for a reason... We all know how much attention to details and UI paradigms Apple is paying.
An error colored in Green for example would break that paradigm and possibly confuse the user. That being said, I think that a (somewhat) solution would be instead of recoloring the warning/error bubbles, to recolor the theme in such a way that every color would make a strong contrast with red/yellow (ie avoid reddish/yellowish tones) tints.
