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yes, at the moment there is. As SUSE harvester is targeted at the hypervisor consumer by using the underlying Kubernetes/rancher/longhorn/etc. that it is built on you are tying your container workloads to those specific versions and support and maintenance would be a nightmare. Imagine a security patch that fixes a component of a harvester cluster necessitating that all your actual application container workloads go off line. Where as, if there is a security patch for the OS you are installing the kubernetes binaries on and running workloads, if using harvester, that is just a change to your base vm template.

Is there something that prevents using the same kubernetes for both containers and VMs?

As Dave pointed out (Thanks Dave!), the main reason to this is VMs are more manageable.