Hi,
You are correct, the clone option is not available on Switch networks that are under a template.
When using templates, Dashboard provides the Profile feature instead.
This option allows you to pre-configure switches on the template using profiles.
When you add a new switch to the network, you can bind it to that profile and the switch will download the configuration in it.
More information can be found in our documentation:
https://documentation.meraki.com/MS/Deployment_Guides/Switch_Templates_Deployment_Guide_(CVD)#Switch...