There shouldn't be any reason that you can't do it with Flyway, but I would be concerned about fighting Flyway a bit. I use Django a fair bit and I honestly don't see a good way to make this approach work for Django, not suggesting that you can't, but you would be fighting Django a fair bit, it's not really how it's designed to work.
If you don't have en ORM, then this is actually much much easier to do right. I'd design the initial schema, either by hand or using some pgAdmin, TOAD or whatever you database has. For there on everything is just hand written migrations.