No change that I have been advised of. I do have some good news for you on THAT specific app though if you are dealing with Macs and not iPads.
OmniGroup has been an Apple Developer since the NextSTEP days. I know for a fact that you can contact OmniGroup explicitly outside the App Store and buy a license for OmniGraffle Pro.
You can download their product for free and then embed a license key in a file and include with your installer once Omni provides it. I did that for years with OmniOutliner until we retired the software in our district. The app store for them isn't the only deployment vehicle for their software. Alas, if you are on iPads, the App Store is the ONLY vehicle.
Contact OmniGroup at 1-800-315-6664 and talk to them about obtaining OmniGraffle Pro from them directly for your Mac fleet. Then you have an installer that you control outside the store. If you are dealing with iPads, your question still stands though and, no, there is no way to do In-App Purchases through the VPP Store as far as I know. If you are dealing with iPads, you could ask Omni if they will post a "fullfile" version of OmniGraffle Pro though at a higher cost in the App Store...that way you don't have to mess with In App purchases.
hope it helps,