It turns out that mage.exe does not have the ability add the trust URL parameters attribute. VS and MageUI.exe can both do it, but if you need to use mage.exe (i.e., build script) then you need to directly modify the XML files. I found a thread on MSDN that contained the following PowerShell approach which works well.
[System.Xml.XmlDocument] $manifest = new-object System.Xml.XmlDocument
$manifest.load( (resolve-path $deploymentManifest) )
[System.Xml.XmlNode] $updateNode = $manifest.assembly.deployment.subscription.update
$updateNode.RemoveAll()
$updateNode.AppendChild($manifest.CreateElement("beforeApplicationStartup", "urn:schemas-microsoft-com:asm.v2"))
$trustUrlParameters = $manifest.CreateAttribute("trustURLParameters")
$trustUrlParameters.set_Value("true")
$manifest.assembly.deployment.SetAttributeNode($trustUrlParameters)
SaveXML "$deploymentManifest" $manifest
#Sign the mangled deployment manifest
mage -sign "$deploymentManifest" -CertHash $signingCertificateThumbPrint