A root deployment is a deployment of only one VCLGroup toward an agent, that is, one VCL loaded into Varnish. The deployed VCLGroup will be responsible for domain routing. This is basically deploying one single VCL into Varnish.
When deploying a VCLGroup as a root deployment, the agent will not accept any other deployments to that agent. This means that any other VCLGroups that potentially could be deployed to the same agent will not validate successfully.
The default way of deploying a VCLGroup is a none-root deployment, also known as shared/cloud deployment. This type of deployment shares a Varnish between multiple VCLGroups with different domains. The domain routing is handled automatically and for each request, the host is matched to the corresponding domain and routed to the correct VCLGroups VCL.