Bug description
Reopening of #30807 hoping to get some feedback this time.

When setting a cluster dnsDomain for kubernetes that is different from the default cluster.local and a cross-namespace Fully qualified service name is used in a VirtualService then istioctl analyze will always print an ERROR IST0101 Referenced host not found

This is true for any value of the dnsDomain other than cluster.local , even cluster1.local

Note that the configuration in the envoy proxy seems to be applied correctly

The cluster is created using kubeadm

• setting the value of networking.dnsDomain to a custom value ( cluster1.local )
• Istio Resource is customized with the custom dnsdomain
  • meshConfig.trustDomain
  • values.global.proxy.clusterDomain
  • values.global.trustDomain

I think those are the right settings for the custom dnsDomain and i could not find any other place where i should change

[ ] Docs
[ ] Installation
[x] Networking
[ ] Performance and Scalability
[ ] Extensions and Telemetry
[ ] Security
[ ] Test and Release
[x] User Experience
[ ] Developer Infrastructure
[ ] Upgrade

Expected behavior

No error is printed unless there is an error

Steps to reproduce the bug
Steps are complex to be completely listed here so I created a GIST , this steps use a test repo of mine to help with scripts and setup

• Create a kubernetes cluster with a custom Dns Domain != "cluster.local"
• Setup IstioD , using the same dns domain in the right settings
  • meshConfig.trustDomain
  • values.global.proxy.clusterDomain
  • values.global.trustDomain
• Create workloads and services in 2 namespaces with istio-injection enabled
• Create a VS in 1 namespace with a destination host in the other namespace using a fully qualified name service-name.namespace.svc.customDnsDomain
• run istioctl analyze and check that you get the IST0101 error
• Check that your virtualservice has actually propagated to the envoy proxies

Version (include the output of istioctl version --remote and kubectl version --short and helm version --short if you used Helm)

• Istio 1.5.10 / 1.6.14 / 1.7.7 / 1.8.3 / 1.9.0
• Kubernetes 1.16.15 / 1.9.7

How was Istio installed?

Istio-Operator

Environment where the bug was observed (cloud vendor, OS, etc)
AWS and Kind

Additionally, please consider running istioctl bug-report and attach the generated cluster-state tarball to this issue.
Refer cluster state archive for more details.