The PKP applications are written in a homegrown framework, styled along the lines of an MVC application. Generally, URIs map against the "pages" folder, which is split in two: either under the root application directory, or in the shared library (lib/pkp) directory. (Request URI mapping can also be handled by plugins.) From the "pages" folder, use the "index.php" to find the Handler, which then generally calls the classes from the application and shared library.
For your particular question about the mounted folder, can you confirm that your web user has access to this mounted location? You'll need to consider not only file/directory owenrship and permissions, but also any PHP restrictions on traversing the filesystem.