I'm having a similar issue along with another piece to add to the pain; was able to include the lrreg file to include the package when it was lightroom v5.2 and the registration was silent. Now when packaging 5.3 using the creative cloud packager (for windows) and launching it prompts for the country and displays our serial #. Adobe mentioned to me that lightroom is part of the exception so you have to install the msi in the build folder first and then run the command for exceptiondeployer (when deploying from sccm). I have tried everything to get this to install and nothing works. The code for running the msi with the exception deployer will not work.
When manually installing each msi, lightroom will install successfully. So then I have tried the provisioning toolkit thinking that would register the product and not prompt user for registration but that doesn't work either.
HELP - anybody?!?!? This has been driving me crazy for weeks now.