Is there a way to have Workspace (DaaS/Cloud) either perform resource deduplication (probably a no) or have Workspace allow us to talk to different onPrem CVAD Sites? Customer has two CVAD sites (primary/DR) and we add them as separate sites in Workspace and Workspace shows us all the apps, as it should, which are duplicated since notepad is in primary and DR site. I thought maybe a custom URL but i doesn't seem to allow me to choose which CVAD site to aggregate. Ideally Workspace URL A goes to OnPremCVAD Site A and URL B goes to OnePremCVAD Site B. Any other options available to us?

Unfortunately workspace doesn't do site aggregation like storefront. Site aggregation in workspace is really only there for migration to Daas/Workspace. If you r customer really wants it to be like storefront hey should probably continue to use storefront. If having separate icons is ok then yes just name them differently.