I think you're oversimplifying the problem they had, and I would encourage you to dive in to the details in the article. There wasn't a problem with the database, it was with the query used to generate the configs. So if an analogous issue arose with a query against one of many ad-hoc replicated sqlite databases, you'd still have the failure.
I love sqlite for some things, but it's not The One True Database Solution.
It’s not a terrible idea, in that you can test the exact database engine binary in CI, and it’s (by definition) not a single point of failure.