What about all the important things you need in a database such as multiuser/remote access and other such things?
What do the "sqlite in production" people do when they need to examine the database/resolve an issue/do development? Also what about the limitations of sqlite in modifying database structure?
The simple answer to your question is you don’t. And if you do need them you don’t use SQLite.
Can you even redeploy a sevice like this without downtime?
Why can't you just use a copy of the database when you need to examine it or resolve issues?
None of these things have anything to do with being a "toy" app or not. They are matters of scale and business requirements. But that's the point isn't it? There are plenty of non-toy systems where none of these requirements apply.
Plenty of very successful business and applications could handle a brief downtime for deployment. Plenty don't need multiple users or remote access, plenty have reasonably small databases.