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I might be missing something but I wonder why customer expects these host being ignored in "Host Configuration Chart"? If they don't run puppet, we don't have any puppet report for them therefore they are listed as hosts with no report. This chart is related to configuration status where configuration means configuration management, puppet in this case. Similarly to this, there's Host Subscription Status.
If you need to filter some hosts in widgets, you can use a filter on top of the page. E.g. "compute_resource != vmware" which will limit widgets to display only hosts not from vmware compute resource.
I tent to consider this as not a bug but before closing, I'd like to hear from the reported if I'm missing something or this explains the behavior.
More than 6 weeks has passed since a NEEDINFO has been requested; therefore, closing this bugzilla. If the issue continues to exist on the latest Satellite 6 release, please feel free to re-open providing additional details. Thanks!