Openhab.cfg for system values

Do i understand correctly that system values like

Should now go to runtime.cfg?

yes, to conf/services/runtime.cfg.

Note that many of those settings now need a org.eclipse.smarthome prefix. You can find the default settings in runtime/etc/services.cfg (this file is not meant to be edited, it is rather like the openhab_default.cfg file in OH1.