Trying to out-specify problematic upstream Drupal 6 styles at the theme level is a nightmare. Instead we will just replace them with SASS _partials.
For example, to override "/modules/system/system.css"
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Add a stub to theme.info to prevent loading. Note: The path doesn't matter, as long as the file name matches the default stylesheet won't load. Don't forget to clear your cache.
stylesheets[all][] = kill/system.css
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Copy the original CSS file to theme and rename it as a SASS partial. To keep things simple, I keep all of these files in a single "drupal" subfolder and renamed to reflect the original path. In this case the file would be:
/scss/drupal/_modules-system-system.scss
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Import this partial into the main SASS file.
@import "drupal/_modules-system-system.scss";
Now you can safely hack these files into submission.