As of today, extensions are packaged and deployed at the same time, directly from Shopify CLI. New app-level extension versioning will help you to keep better track of your app's iterations, and allow you to easily revert to previous versions.
Until September 5th, you can opt in to get access to simplified deployment. Simplified deployment is available in Shopify CLI 3.48.
On September 5th, all apps will automatically be opted in to simplified deployment.
Learn more about simplified deployment.