At first, Full xLights Control basically would "clear" the ports and then upload the the configuration for the ports that are actually defined in xLights. If you had the Set Brightness enabled on a model, then that setting would get uploaded as well. If not, then the brightness setting would not get changed (at least that is how I remember it?)
Now there is a default brightness option and if you have Full xLights Control enabled when you upload your output ports configuration, xLights will set the brightness for every port (except the ones that you have defined with Set Brightness) to the default setting. Should it be setting all ports to the default value or only the ports that are not defined in xLights?
My thoughts are that, for example, you want to manually set your brightness in your controller (not necessarily all the same value) and you don't want to use the Set Brightness option in xLights but you do want to "reset" unused ports because you might move a string from one port to another you would want the Full xLights Control option enabled (to "reset" unused ports), but in doing so all of your ports get configured to the default value in xLights.