Dearest calvingrier: (A name almost as strange as dickelbeck)
Your example *.SES files both "back import" into PCBNEW now. I am ignoring the structure_out element. In your example, this was a mere replication of the boards original layer definitions, which remain the same after the round trip. This will get you further. You will have to build from source to test the changes, or download one of the nightly binary pre-built snapshots. Dick