Is it possible to make appx to store its packages in program files folder insted of windows apps folder during installation?.If it is possible how can we make it?
No, you can't control this. Windows handles this logic.
The entire purpose of the AppX packages was to limit the thinks you can mess with (as a dev or end user), and to abstract the files system for the end-user. That is why they replace the notion of shortcut with "application" and why an end user can't browse to the install location of the application.