The customer has autoscale capability set at cluster level and not at org level. The CS backend checks for the capability at the cluster level first according to this code: 

if cluster.SubscriptionID != "" {
{{ enabled, err = accountsManagerClient.IsClusterCapabilityEnabled(ctx,}}
{{ cluster.SubscriptionID, auth.AutoscaleCluster)}}
{{ } else {}}
{{ enabled, _, err = accountsManagerClient.IsCurrentUserOrgCapabilityEnabled(ctx,}}
{{ auth.AutoscaleCluster)}}
}

Ideally, the customer should be able to autoscale machine pool on the UI.