The native vlan must match on both sides of the link. We are using an unrouted vlan (vlan 5) on interfaces. You will need it if you ever start using stackwise virtual and multichassis etherchannel with the 9300 switches. If you have to add a vlan to a trunk link, the interface goes down for about 10 seconds. We found out from Cisco that with 9300 switches running MEC, and connecting to Cat 9500 and 9600 switches running Stackwise virtual that if the native vlan is also used in the trunk link, you will have a short outage. This is what we do:
Switchport trunk native vlan 5 (no SVI for that Vlan. Only created in the vlan database)
Switchport trunk allowed vlan 100, 1001
Switchport mode trunk
Since vlan 5 is unrouted, you can use it in the whole network (even if you have over 5,000 devices like we do) Remember that with Cisco, the native vlan is an untagged vlan. Therefore, since we are using vlan 5 as native, even if you were to add it to the trunk link, there would be no packets tagged with vlan 5. I could tell you other stories about that, but I have some stuff to get done this morning.
Hope that helps
