Glad you figured out a novel solution. I am surprised that Suricata does not complain about the duplicate output sections in the suricata.yaml file, though. I've never investigated the parsing portion of the YAML code in the binary, so maybe it's the case that the last value read from the file is the one stored in the in-memory configuration array (overwriting any previous value for the same parameter).
I would expect the ALERTS tab in your custom configuration to be blank and not showing any alerts. As I said in my earlier reply, the alerts.log file is how that tab gets populated in the GUI. You will still see any alerts in the other configured output logs, though, such as EVE.