nm-cloud-setup automatically detects routes, addresses and rules and configures them on the device using the emphermal Reapply() API. That is, it does not modify the existing profile (on disk), but changes the runtime configuration only.
As such, it used to wipe otherwise statically configured IP addresses, routes and rules. That seems unnecessary. Let's keep the configuration from the (persistent) configuration.
There is of course the problem that nm-cloud-setup doesn't really understand the existing IP configuration, and it can only hope that it can be meaningfully combined with what nm-cloud-setup wants to configure. This should cover most simple cases, for more complex setups, the user probably should disable nm-cloud-setup and configure the network explicitly to their liking.