Sydney Trains GTFS-R Version 2

Sydney Trains have completed work to upgrade their vehicle position and trip update feeds to GTFS-R proto V2.0. The feeds are available in production now:

https://opendata.transport.nsw.gov.au/dataset/public-transport-realtime-vehicle-positions-v2
https://opendata.transport.nsw.gov.au/dataset/public-transport-realtime-trip-update-v2

The attached proto file in these datasets should be used to consume these feeds. It includes TfNSW assigned GTFS-R extension 1007 for extra info such as carriage based occupancy levels.
The Sydney Trains V1 feeds will remain in use until 12 November 2021, at which time they will be deprecated. All users will need to migrate to the V2 feed by this date.

is there one .proto file which works for all GTFS-realtime feeds (with and without TfNSW-specific changes)?

Not yet. The intention is to eventually align all feeds to use the same proto. The ones currently in use are on our documentation page. Documentation | TfNSW Open Data Hub and Developer Portal