Istio Virtual service - enforce specific api version
I have managed to solve it myself later that day, I had to disable one of the apigroups within the specific crd that is responsible for the given object.
In that case it was editing:
kubectl edit crd virtualservices.networking.istio.io
And then change:

  versions:
  - name: v1alpha3
    served: true
    storage: true
  - name: v1beta1
    served: true
    storage: false


to

  versions:
  - name: v1alpha3
    served: true
    storage: true
  - name: v1beta1
    served: false
    storage: false


Then on redeploy I had the correct apigroup which I wanted.