A proof of concept.
If you cant't/won't use the apps Migration files this workaround can be helpful for you.
We assume you have a clean Database without any Migrations applied and a Project named my_project that you are working on.
Add the below snippet in your settings.py right after INSTALLED_APPS.
This tells django to use migration files from the module in my_project.migrations.<appname>.migrations.
If you now run ./manage.py syncdb you custom Migration files will be created in /my_project/migrations//migrations`.
👍 Cool!