I\'m testing my assumptions at the moment. I have my Asp.Net MVC application located at www.myapp.com/app
and a third-party CMS system on www.myapp.com/
I don't think this is possible from PowerShell, but I might be mistaken. Looking at their publish code here https://github.com/Azure/azure-sdk-tools/blob/master/src/ServiceManagement/Services/Commands.Utilities/Websites/WebsitesClient.cs#L1136-L1168
and also here https://github.com/Azure/azure-sdk-tools/blob/master/src/ServiceManagement/Services/Commands.Utilities/Websites/WebsitesClient.cs#L1218-L1229
they don't have a parameter for the app name, and the code in the second link builds the site name/slot manually.
I would say open an issue here https://github.com/Azure/azure-sdk-tools/issues for this and somebody from the Azure PowerShell team should look at it.