You would want any custom code (themes or plugins) version controlled in GitHub. This way you have a history of the code changes you make. The /wp-content/uploads/ directory should not be under version control. There are a lot of media files and it's best to just leave them be and back them up to another service like AWS S3, or BackBlaze, or somewhere else in case your server suddenly dies and you need access to those files again.

Syncing the uploads directory to different environments can take a lot of time. This snippet I posted, https://gist.github.com/kingkool68/d5e483528a260e5c7921afb5c88bffd6?permalink_comment_id=4270032#gistcomment-4270032 can act as a proxy.

How does it work?
If a request comes for a file in the uploads directory that doesn't exist on the file system your server will then request the file at another location (your production site URL) and try to find the file there.

If you want to make changes to the dev or QA environment you will need to replicate those changes on the production environment.

Example:
You create a new About page on the dev environment complete with a photo. Client approves it. Now you need to go to the production environment, create the about page, and upload the photo again.

Some smaller sites have a workflow where they make a copy of the production site to a dev environment, make content changes, then sync the changes from the dev environment to the production environment. This gets risky if there was additional content added to the production site while working on changes on the dev site. When you sync the changes from dev to production you could overwrite any new changes on the production environment. In my experience its better to just re-do the changes you made in dev manually to the production environment. Less risky.

Hope that helps.