So from what or how I understand it, what will happen is you will get hold of GDR3 Pre Release, it might be a different build number to the GA or Release Candidate version of GDR3, this will then allow MS to patch your Pre-Release to GA/RC version via OTA with Bittersweet Shimmer from Nokia (tied together in a rom from the Nokia Servers)
I hope that helps or at least resolves your concerns
p.s. for anyone who isn't sure about Amber - Amber is not part of the OS its mainly Firmware with bespoke apps/settings which will be preserved when updating to GDR3 just like any other normal update process,
if you flash the Phone with this you will loose all settings, the Firmware will remain however therefore when you have a fresh version of GDR3 installed you just need to get hold of the updated Nokia System Apps which will re-enable any of the new functionality that might not be part of the base image from which you are flashing with and thus you will receive the same functionality from the phone that you got from your GDR2 and Amber update.
In short - Amber is independent of the OS, it requires a Min OS Version which we will exceed with GDR3 anyway, hopefully though GDR3 is rock solid enough to not break any existing functionality, i.e. Accessories for Nokia has bespoke settings for certain hardware, e.g. JBL PowerUp or PlayUp Speakers, with the updates to Bluetooth Functionality in GDR3 I do not know how this will turn out for Bluetooth functionality on those apps/uses etc etc