For themes, I would believe that hard overwriting is the best solution due to the nature of the changes they make.
For addons, however, I wanted to suggest potentially visiting patch files to apply changes. They would allow for seamless addition of addons and for more addons that may edit the same files without having to have those files merged together on GitHub due to conflicts. If this is something the project would be interested in taking a look at, I would be happy to help as I have wanted to make something similar to this myself for addons and themes.
For themes, I would believe that hard overwriting is the best solution due to the nature of the changes they make.
For addons, however, I wanted to suggest potentially visiting patch files to apply changes. They would allow for seamless addition of addons and for more addons that may edit the same files without having to have those files merged together on GitHub due to conflicts. If this is something the project would be interested in taking a look at, I would be happy to help as I have wanted to make something similar to this myself for addons and themes.