Namely, it doesn't support configuration via CLI or env vars, which means you have no option but to generate a file to be loaded in. To be fair, that's kind of a newer pattern. Also, multi-DB PgBouncer is a little more insecure than it leads on to be by default, along with a few other things you learn quickly as you handle larger and more complex use cases. It's not bad, just not as good as it could be in my opinion.