The issue here turned out to be that this cluster had the following apiservices installed:
kubectl get apiservices | grep -i custom
v1beta1.custom.metrics.k8s.io cattle-monitoring-system/rancher-monitoring-prometheus-adapter True 80m
v1beta1.external.metrics.k8s.io custom-metrics/custom-metrics-apiserver False (ServiceNotFound) 20d
v1beta2.custom.metrics.k8s.io custom-metrics/custom-metrics-apiserver False (ServiceNotFound) 20d
I removed v1beta1.external.metrics.k8s.io and custom metrics started working correctly.