PipelineOptions subclasses defined in the main session could be duplicated

Duplication is caused as a result of the save_main_session option.

This also breaks argparse because same options will be defined multiple times.

Imported from Jira [BEAM-1319](https://issues.apache.org/jira/browse/BEAM-1319). Original Jira may contain additional context.
Reported by: altay.

Start by tracing save_main_session handling for PipelineOptions subclasses defined in the main session, then inspect how argparse options are registered. Reproduce the case where subclasses are duplicated and the same options are defined multiple times. Done means the duplication and resulting argparse failure no longer occur.

Written by the indexing model from the issue text.