"General best practice is to leave the native VLAN on a trunk port unused"
It is best design practice not to leave native vlan 1 on your trunk ports, even when you have changed all other ports to other than vlan 1, and sure not to use vlan 1 as your managment vlan. But I have never heard anything wrong with use of a different native vlan.
Where is that stated as best practice not to use native vlans? That sure is not cisco gospel.. Maybe that is the gospel according to cmb ;) hehehe
As a way of graphing traffic so all your traffic is in a specific tagged vlan vs the native vlan that would show all traffic going over that interface even tagged ok very clever solution to the graphing oddity, but I wouldn't agree that its best practice to only use tags..
I can think of one example where its going to cause you a problem not using native, the unifi accesspoints do not allow you to set vlan tag on their management IP. They have to be untagged, ie native. Sure doesn't have to be vlan 1, but they do not allow you set tag for the IP of the AP.. This might be considered a design flaw, and it should be an option to set tag on this - maybe in the future but currently if your not using native vlan here you would have issues. Quite sure there are other such devices, but off the top of my head that was the first one that came to mind. That would require trunk and tagged traffic to the device, but also untagged traffic.