Grading exceptions should not unconditionally override `bonus_points` etc.

If they do, then any changes in the flow YAML must manually be copied to the exceptions.

The issue names grading exceptions, flow YAML, and the `bonus_points` setting, but no file, test, or entry point. Start by locating the grading-exception handling and how flow YAML values are applied. Done means changes in flow YAML no longer require manually copying unchanged values into exceptions, while explicit exception behavior remains clear.

Written by the indexing model from the issue text.