Hi Pik Lee,
As a security measure, files in the App_Data folder are not served by the Web server. However, the ASPNET or NETWORK SERVICE user account are granted Read and Write permissions for App_Data. We have plans to make it possible to install a website template from Sitefinity marketplace directly and therefore we need to have full access to the folder the website will be installed to. It will be also possible to export websites and upload them to the market place but they will need to follow the website template structure.
The schema in the Designer's guide is designed to serve website template installation so there is no confusion once this functionality is available. Because files in the App_Data folder are not served by the Web server, we have mapped them to be served as if they were in Sitefinity folder. The schema is not mandatory, it is recommendable. You are not obliged to follow it.
Let us know if you need further help.
the Telerik team