I have a WP8 to test my developed apps.
I have 2 apps installed: one deployed by VS2013 and another by Windows Store Beta App.
The app installed by VS2013 appears on IsoStoreSpy or Windows Phone Power Tools programs and I can copy the database.
The other one installed by Windows Store (beta app download), I can't find the Database and the ID of the app not appears in IsoStoreSpy or WP Power tools.
Is there any problem with apps installed by store to get the data from isolated store ?
That's the drill..!
You can not play with any of internal Data of Windows Phone application which is installed from Windows Phone Store, irrespective of the app is BETA or Public.
Once you upload the app package to Store, Microsoft will Encrypt the App package and make it non Extractable anyhow..! Whereas the App Package generated by Visual Studio is extractable and can be accessed by any developer tool as you mentioned like WP Power Tools.
That's the security purpose.
For more reference check below links.