I was going crazy trying to figure out how to get applications to launch with the credentials of the user that was logged on to the Web Interface. Passthrough worked fine for the initial logon to Web Interface, but after that a Windows logon box appeared for each application that was launched.
Apparently there is no way to configure this in the Access Management console. However, I did finally find a way to modify the default.ica file (located at "C:\Inetpub\wwwroot\Citrix\XenApp\conf\" in my environment) to allow full passthrough.
Assuming you have already enabled passthrough authentication to the Web Interface web site in the Access Mangement console, simply add the following lines under the [WFClient] section in the default.ica file:
EnableSSOnThruICAFile=On
SSOnUserSetting=On
Do this for every Web Interface server and it should work immediately!
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