I always thought that Debian is already on git, so this confused me. How is source control currently (or was) done with the Debian project?

The short answer is that it's not.

The longer answer is that a lot of people already use Git for Debian version control, and the article expands on how this will be better-integrated in the future. But what goes into the archive (for building) is fundamentally just a source package with a version number. There's a changelog, but you're free to lie in it if you so wish.