I understand the internal URL in Azure Application Proxy is restricted and inflexible. It cannot have a path, basically it must be a root URL for the URL rewriting to work properly. No problem. That's the administrative side. In theory, from the web service and DNS, you should be able to manipulate whatever you need so that a nice and neat internal URL will work internally and be given to Azure Application Proxy. For example:
https://myapp.myserver.com/apphome/messydefaulturl/default.aspx
Should be able to be boiled down to an internal URL as:
In reality, it's just not always possible for numerous reasons, and for this to be a feasible solution it needs to accommodate an extra layer.
I think the answer is an extra field in configuration with simple concatenation for when the user clicks the link. My application works when I append the rest of the /path/path.aspx manually, so I can't think of any reason I shouldn't be able to modify the "App Shortcut" in the portal.
In summary, for the user-facing tiles of each published application, administrators need to be able to add additional path parameters (at https://myapps.Microsoft.com)