I'm not sure I understand this entirely. We use a configuration repeatedly, which I copy and modify every few months, to uninstall the previous version of an app and deploy the new version, as it is a crappy install-shield installer that doesn't know how to upgrade itself in place. We've never seen it fail to uninstall first (software deployment #1) and then install the new (software deployment #2) in the proper order even though they are part of a single configuration.
I have also designed a few batch scripts to add intelligence to other configurations, which may solve the need for others. For instance our Office 2010 push configuration copies the files, and un-7zips them as a pre-install script. Then it installs. Then as a post-install script it runs a batch file I designed for auto-activation online. Works like a charm.
Just offering food for thought. Cheers.