If you drop your app's config file in /etc/ and nothing ever touches it, isolation isn't really buying you anything. If something does, that could still be what you want to happen.

For example, suppose there is a P2P app that can operate either by having you forward a port from your router (which is not always available) or by operating as a Tor onion service. To do the latter it has to modify Tor's configuration so that it allows incoming connections to the application's port. It's something you want to happen, it's something the package can clean back up again when it's uninstalled, but that doesn't work if the two otherwise independent applications have their configurations isolated from each other.

So it's still the permissions problem.