Themes cannot control the background of the report notifications in the info header, often resulting in problems like this one:
The outline and shading of the report can be controlled via the options in themes > user interface > box, however these give very limited control.
Even some of the bundled official themes have rather odd looking reports because of this, for instance Back to Black:
This patch doesn't add new controls to the theme options, but instead sets the report background color based on the inner color of the box section, and the part of the backgound under the icon is controlled by the item color of the box section.
The only problem with this that any changes to the report colors will also affect the box UI elements. If this is too awkward, then it may be better to add a new separate theme option for reports. (not sure about this, feedback much appreciated of course ;)
This patch also makes the color that the report briefly flashes themeable using the existing theme controls for highlighting lines in the info window.
The idea is to make the highlighted line colors consistent with the report colors. The current line selection color in the info window (blue) could conflict with this, so I propose that it be changed to orange to stay more consistent with other parts of blender.
These changes are not in the patch (yet).