So you don’t have HA. You should let the yaml as it is. No modifications. The command sections are basically the Cluster configs.
They are using the default config. If you don’t explicitly change the configs via those flags it will run the default values. So you will have 3 groups.
Reasons for this can be two. Or you are confusing something at some point. Or you ran that same yaml once and modified it later as overwrite. But modifying the YAML does not modify the configuration that was passed in the first moment.
Solution. Export your data. Delete everything, and start from scratch with your desired config. Be it th default or HA(by not touching the yaml).
BTW, If you want to run a cluster without HA you should take the example without HA. Don’t try to modify a YAML. You can end up breaking everything unless you really know what you’re doing.