Suggestion to JA:
Implement a CSS file like Gavick does. It should load last and could overwrite anything cascaded before. Just see how Gavick has done it.
Why?
Sometimes people need to change only few classes (i.e. logo, some color, some width). However, by doing that in the template directly, it is then hard to upgrade. I know you are going to tell me that I can create a sub-theme. However for that I also need to copy everything (i.e. all the css, if not using the default theme color). That way, if change happens, I will need to update the sub-theme as well. Just for few lines. I know you are going to tell me to use the JA Extension Manager, but still…
For sites with minor changes of the default themes (any), a file override.css will be like a breeze solution. Please consider it.