I have not really thought about source control SQL Agent jobs with a VCS as such.

What we tend to do is to keep the SQL jobs very simple - a single step that calls a stored procedure in a database.
The jobs are prefixed with the database name so that one can easily see where they belong.
General jobs, like backups either don't have a prefix, but sometimes we do add something like 'General_' or 'Maintenance_'.

So most SQL job really lives in a stored procedure inside the database, which would by definition be the correct version.
Jobs are scripted to file for backup purposes with separate files for 'General' and database-specific jobs.

I am interested to see what other people are doing!