sometimes the native vlan is required for example a cisco iOS switch passes protocols like cdp vtp etc on the native vlan. i don't think meraki "needs" it but just keep the native the same between two switches then ur ok. yes you can add native also to allowed vlan list , its best to choose a vlan your not using for cliënts. https://documentation.meraki.com/MS/Port_and_VLAN_Configuration/Recommended_Configuration_for_Trunk_Link_to_Non-Meraki_Switches
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