The Configuration Wizard has no knowledge of the extra columns in the base table, and the SSIS_Config view it is updating doesn't include the EnvironmentEnum column so anything it inserts will have to default to EnvironmentEnum=0. In some cases it will do an update instead of an insert and only change the value for one environment, but that will be based on where BIDS is running and not the environment you had in mind when you made the change. But it really isn't safe to let the Configuration Wizard stomp on existing configuration sets.

You can use the Configuration Wizard to add new configuration items with a dummy ConfigurationFilter value, then go to the SSIS_Config database and see the results. Then you can split them into multi-environment values if desired, and move them into an existing set by updating the ConfigurationFilter column. Then go back to the package Configuration Wizard to remove the dummy config set.