Dataflow specific pipeline updates are not reflected in the pipeline proto

More specifically the to visits here.

[https://github.com/apache/beam/blob/master/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py#L566](https://github.com/apache/beam/blob/master/sdks/python/apache_beam/runners/dataflow/dataflow_runner.py#L566)

These have to be done before creating the pipeline proto for Dataflow to be able to correctly generate job requests from portable protos.

Imported from Jira [BEAM-10933](https://issues.apache.org/jira/browse/BEAM-10933). Original Jira may contain additional context.
Reported by: chamikara.