I am running DNA Center Version 126.96.36.199-72328 and have just noticed an odd thing with native VLANs,
When you show the switch front panel view in Inventory and hover over a port one of the fields in teh box that pops up is "native VLAN".
For normal access ports this is populated with the correct VLAN (i.e. whatever "switch-port access vlan X" is set to. The same for trunks between two Cat 9K switches (though all of these are set to native VLAN 1) on this LAN.
However we have some edge trunks going to Meraki MX67s with native VLAN set to 2001 and nothing is displayed in the native VLAN field apart from "-".