Why not generate the secret key every time Flask starts?

The secret key is used to sign the session cookie. If you had to restart your application, and regenerated the key, all the existing sessions would be invalidated. That's probably not what you want (or at least, not the right way to go about invalidating sessions). A similar case could be made for anything else that relies on the secret key, such as tokens generated by itsdangerous to provide reset password urls (for example).

The application might need to be restarted because of a crash, or because the server rebooted, or because you are pushing a bug fix or new feature, or because the server you're using spawns new processes, etc. So you can't rely on the server being up forever.

The standard practice is to have some throwaway key commited to the repo (so that there's something there for dev machines) and then to set the key in the local config when deploying. This way, the key isn't leaked and doesn't need to be regenerated.

There's also the case of running secondary systems that depend on the app context, such as Celery for running background tasks, or multiple load balanced instances of the application. If each running instance of the application has different settings, they may not work together correctly in some cases.