I believe this is not the meaning, generally avoiding using VLAN 1, and only allowing VLANs that will actually be used in the Trunk, but you do not need to avoid the native VLAN.
I am not a Cisco Meraki employee. My suggestions are based on documentation of Meraki best practices and day-to-day experience.
Please, if this post was useful, leave your kudos and mark it as solved.