Prior to 4.10, the documented way to specify an override like this:

{"kind":"Deployment","group":"apps/v1","name":"machine-api-operator","namespace":"openshift-machine-api","unmanaged":true}

That turns out to be because the "group" field was ignored altogether. After that was fixed by OCPBUGSM-37125, the above no longer worked. Now you must specify:

{"kind":"Deployment","group":"apps","name":"machine-api-operator","namespace":"openshift-machine-api","unmanaged":true}

i.e. only apps and not apps/v1 is accepted. The docs were eventually changed to match the new behaviour by https://github.com/openshift/enhancements/pull/982.

Given that there is no separate version field in the override, if we ignore the version in the manifest's apiVersion we should probably ignore it in the override's group as well, particularly since this used to work and be the documented way of doing it.