There is a main operator responsible for all the databases. It handles configuration changes, provisioning pods and slowly rolling out changes. In kube we model this with a custom resource we've defined called a KeyspaceShard which represents a named set of database instances that should participate in replication together. Once provisioned, the pods know how to hook up and detach from Vitess without requiring further involvement from the operator. Vitess handles backups and maintains the replication topology. "Complicated" is an apt description of what it does but not "complex". Evicting a database pod and letting the system reschedule and converge is a routine operation that doesn't cause much concern.
Migrations are done with gh-ost, which has its own custom operator that manages the lifecycle of the migration and ties into self service tooling we provide that is integrated with our build and deploy system.