The post you reference only solves issues where the application has an internal manifest requesting elevation and doesn't really need it.
If the app attempts to perform certain actions, you'll get the UAC prompt anyway. You should run the package analyzer in AppV_Manage on the package to see what you are dealing with. Manifest elevations are shown under Applications.
UIAccess type elevations are also shown in the Analyzer. These can't be solved using the method of the mentioned post. Either an external manifest file is needed (a technique that probably requires a GPO to allow), or a trick involving VFS might help.
Or you just turn UAC off on target machines and hope for the best.