On production and really most dev servers we're doing a DB backup/restore, so we never need to do this. The automated tests are the only time it's regularly applied, and that's done through the UI (though it's automated test code doing this). I view it mostly as useful for catastrophic failure type situations since it'd be a real pain to re-create that. The LK folks can hopefully help debug this, but you really should not need to be resetting those with new builds or when upgrading to new releases.

LabKey doesnt typically have static config files to easily bootstrap new pre-configured instances in quite the way you're describing. The nature of a LK server (which could hold all sorts of different projects) is a little different than many single-purpose servers. LabKey folder import/export is the closest thing to this, and it likely includes study permissions. You might consider that if you do need to do some type of programmatic process to create a new pre-configured server instance, though to my knowledge not a lot of groups do something like this.