Or is this just so that everyone can upgrade to universal for free, no matter which app they'd bought before (assuming they'd only bought one)?
You're correct that at the moment Files Pro and Documents Pro are essentially identical. Because Apple provide no means of "upgrading" users to another application we had no choice but to keep both apps on the App Store. "Files HD" didn't seem quite right for a universal app, hence the name change.
Going forward we plan to give Documents Pro more of a business focus. So for existing customers who have both apps we'd probably recommend staying with Files Pro.