If you need to preserve data between the application versions then you still get all the headaches with MongoDb (either migrating the data or supporting multiple schema versions when you read the data, oh the fun!).
If you don't need to preserve data between the versions then you don't need to write migrations scripts in SQL, just scrape everything and pretend it's the first version of application.
This would save you time on picking the db, schema changes or even migration changes in Mongo. You don't have to worry about bad documents from an earlier app revision.
I have ~40M documents, and it’s still a subset of what I’ll manage in production. It takes a few hours to load them in the database.
I am trying to remember if I ever built a prototype that got rewritten. Probably not.