Perhaps you could explain your problem a bit more.

You give an example of static configs:

     - https://app1.customer1.exmaple.com
     - https://app1.customer2.exmaple.com
     - https://app2.customer2.exmaple.com


To kubernetes, what are these? Services? Endpoints? Something else?

kubernetes_sd_config has roles 
<https://prometheus.io/docs/prometheus/latest/configuration/configuration/#kubernetes_sd_config>
 
for ingress, service, endpoint.  Do these not work with Istio?  Can you 
show what you've tried, and explain what happens when you try them?

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