header-checker: Cleanup create_reference_dumps.py

This commit refactors the `main()` function, cleans up several
indentation or spacing errors, and rewrites some code in Pythonic way.

Test: ./tests/test.py
Test: ./utils/create_reference_dumps.py
Change-Id: Ie654187bff5b5c49b421814efab0e8f308c93fa8