Effectively forward porting changes of core theme: Git Three Way Merge with Core Changes?

I am working on Magento (not asking this on magento.stackexchange.com because it is more git related).

Sometimes it is unavoidable to change files from core theme.

It works (simplyfied) like this

1. That is the core file: vendor/magento/module-theme/view/frontend/templates/message.phtml
2. I copy it to app/design/frontend/My/Theme/default/Magento_Theme/templates/message.phtml
3. Now I make a git commit of the file "Original taken from the core"
4. Now I make my changes
5. When upgrading to a new Magento version, the vendor/magento/module-theme/view/frontend/templates/message.phtml is probably updated (via composer, the file is not in my git)
6. Now I am looking for a way to either port the new changes from the core (from the vendor folder) to my custom file. Or to re-apply all my changes to a fresh copy from the core.

I was already pretty successful with creating a patch between my "Original taken from core" commit and the current version, copying the new original from core and applying the patch. I did all this manually and I am wondering if there is an more automated way.