At this time my comfort zone is managing each theme and plugin as a separate Git repository and using WP Engine to rollback if I break anything during a WordPre

At this time my comfort zone is managing each theme and plugin as a separate Git repository and using WP Engine to rollback if I break anything during a WordPress/theme/plugin upgrade. WordPress is just upgraded using the 1-click upgrade, and plugins are upgraded using 1-click if they're on the official repository.