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- For more granular on db migration between development and production, I use Phinx (https://phinx.org/). So, development team has no need to touch the GUI via wp dashboard to make any changes. This tool is similar to laravel eloquent, or ruby on rails' active record.
Re. tooling, mostly GitHub, GitHub Actions and an open source tool I built called Sail CLI for deployments and backups.
For premium or private plugins, you can use SatisPress. SatisPress turns a WordPress site into your own private Composer repository, where plugins/themes installed on the site can be exposed as composer packages, and, since it's a WordPress site, the plugins/themes can be updated just like any other plugin/theme on any other WordPress site would be. SatisPress requires(?) you to authenticate to be able to pull packages into your project - you can leverage Composer's auth.json to automate authentication.
My current setup is similar, but with a src folder that builds into the theme dir. Good idea on the modules folders.