Syncthing supports transferring data via untrusted relays (used when two nodes cannot communicate directly) and also supports storing data encrypted on untrusted nodes (those nodes cannot decrypt the data)
The quota includes not just the git repo, but also other services that gitlab offers. In particular the container and package registries are easy to setup in a way that accumulates a lot of data (e.g. by building and tagging a docker image in every commit and not cleaning up old images).
In most cases this will be a misconfiguration and all the quota enforcement is doing is to force people to configure their projects a bit more considerate.
As far as I know, the quota itself isn't new, it just wasn't enforced in the past.