The Bootstrapbase config.php file currently excludes two style.css sheets coming from the HTML block and the grader report plugins. (There also used to be navigation and settings blocks but the changes were rolled back before 2.5 final)
This was done because the CSS coming from these files was tricky to overrule.
Actually the HTML block one is actually very simple. The only reason it's was done like this was because it shared code with the settings and navigation blocks, but those changes were rolled back.
The grader one however might take some more effort. Any shared CSS should be in the styles.css file and theme dependent stuff moved to either Base or Bootstrapbase. It could also just generally be tidied up at the same time, since it has duplication and rules for IE6, 7 etc.