Two helper scripts in the tests folder make this possible.
Use tests/gbk2coords to create a tabular version of the final genbank output, then use tests/compare-summaries to compare two of them.
The latter script is a small wrapper around diff that removes the numbers from ORF#### gene names, as these numbers can vary and appear as spurious differences.
Example:
./tests/gbk2coords ../verA-results/sample.gbk > ../verA-results/coords.txt
./tests/gbk2coords ../verB-results/sample.gbk > ../verB-results/coords.txt
./tests/compare-summaries ../ver{A,B}-results/coords.txt | less