There seem to be some significant changes to the way Xcode 4.3 needs to be packaged for deployment compared to earlier releases. I just helped a customer through this process and wanted to share our process:
1) Packaging Xcode.app:
Xcode 4.3 is distributed via either the App store, or via Apple's Developer portal as a DMG download. We had better success with the DMG download. Take a 'Normal Snapshot' with Composer, copy the Xcode.app into the Applications folder, Launch and proceed with any install prompts until you get to the normal Launch screen. Close your snapshot, check your sources, and Package as a DMG archive.
2) Packaging any Add-ons you want:
Within Xcode's preferences, there is an in-app downloads section. You might consider packaging these separately by using a 'New and Modified' Snapshot after Xcode has been installed. It seems the end-user doesn't need to be an Admin to install them (they just need an Apple ID with Developer access). So this seems to be optional.
3) Installing the Mobile Device Package:
I'm not sure why, but our Xcode.app snapshot didn't carry over the Mobile Device package that is a necessary addition for Xcode to run. This .pkg is actually located within Xcode.app, and can be installed as part of a larger Xcode install policy using a very simple 'after' script that executes this command:
installer -pkg /Applications/Xcode.app/Contents/Resources/Packages/MobileDevice.pkg -target /
I suppose this could apply to any other .pkg's that show up in this path of future Xcode.app downloads.
4) Uninstalling any previous version Xcode version:
If you are upgrading from a previous version of Xcode that deploys a /Developer path, you will want to uninstall the previous developer tools and developer folder. Apple provides a perl script to help us with this. It should be run in a 'before' script:
rm -rf /Applications/Xcode.app
Hopefully this provides some helpful insight. I owe some credit to my friend Rich at Der Flounder http://derflounder.wordpress.com/2012/02/17/building-a-grand-unified-xcode-4-3-installer/ for some tips, especially on the uninstall scripts.