And what did You expected to get. When You include those entry points you are getting the cmd and regedit, whish runs in the virtual system. So with these tools You can see the files and registry entries which exist only for your package.
If You pack the program with such structure:
-Program Files
_L AppName
___L Folder1
_____L ...
___L Folder2
_____L ...
______...
so on the machine where "AppName" is not installed system CMD won't see these folders in Program Files dir, but the entry point CMD of your package can do it.
The same story about registry.
Earlieas videos off Thinstall were containing some of subscribed tricks, but now I don't see those videos.