I've been using a solution that's working perfectly for me. Unfortunately, the only way is to:

1. Uninstall all the Org installations that you don't want to use (example: delete the Org Elpa installed version if you plan to use the git cloned version). 

2. Advice a package.el function that never auto-installs Org as dependency. 

3. Another advice to never update Org using the package manager (as you would be managing the updates yourself using git). 

Basically the update/dependency-check should not install Org. 

A while back, I did a detailed write-up on this setup: https://scripter.co/building-org-development-version/. With that setup, and modi/org-version-select set to 'dev, I don't have to worry about other Org versions getting auto-installed. 

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