Acrobat products have no way of interacting with 3rd party products. The install assumes you want an Adobe product to own PDF, and the ownership settings can only control which Adobe product does that. If you want another product to own the PDF mime type, you may have to install the other product after Reader or research how to return pdf ownership to the other program through manual registry tweaks that you propagate via GPO or some other method. I don't know how complex that task is.
You might get a better answer than this (I hope so), but that's what I suspect is true here.
Ben