At the risk of being over-simplistic, wouldn't the Acrobat Customization Wizard work better for you folks? We're kind of forced into going that route because we have Acro Pro covered under a separate enterprise license (and a whole lot more of them purchased than CC licenses). It generates an mst file with licensing and configuration preferences, optinally surpressing EULA and registration requests, as well as configuring virtually every option the program has.
It still took me a good part of an afternoon to figure out how to build and deploy Lightroom updates. But that's a totally different story.