3.0 configuration should give precedence to console-handled configuration over the one from config file. After restart it should preserve console settings. The config entered endpoints etc should be added only if missing.
It must be possible to turn this feature off, and return to the current behaviour (for those who still want to stick to config files).
Options for this already exist (fullyRecreateEndpointsAROnStartup ignoreContentsReloadingFromConfiguration) but change defaults in distro, test and update docs to explain this.