My guess is, the Vagrant VM, requires the user "vagrant" to own the files contained within the synced_folder.
When you startup your VM, and run your script to "git clone", vagrant is
trying to clone to a shared directory (which it doesn't have permission to write to).
Rsync suggests that files are rsynced to the folder (through vagrant) and the result is the files are owned by "vagrant".
Who owns the directory and files when you don't use "rsync"?