I was dealing with the same issue here. I Figured out how to setup the Start Screen when imaged, but like you, we will need to make changes to machines in the field w/o reimaging them.
What I found was that you can log in as a user and configure the Start Screen as needed and then copy c:\users\username\appdata\local\microsoft\windows\appsfolder.itemdata-ms to the same location for the default user. You'll need to set it as Read Only in the default user's folder or new users won't get it.
That let us change it for new users on the machine. For existing users on the machine I setup a GPP targeting users that repalced the updated.itemdata-ms in the user's profile with one that we have stored on the Netlogon folder.
The itemdata-ms file should be marked as read-only regardless of the profile that it's in. I haven't seen it work otherwise. It also restores the Start Screen configuration to what it should be when the user logs back in.
I'm still working on getting IE favorites on the Start Screen. Right now they can be added from IE but loading them and then pinning them changes the URL that is used for a lot of them. Kinda like the Heisenberg Principle. Still working that one out.