Michael,
I don't know what is happening with your OWA based on the available information. I believe that reinstalling Rollup 3 will rerun the OWA VDIR powershell and set up OWA Properly for you. It runs for every rollup. If that doesn’t solve the problem, we should escalate the issue and get you support.
We have also reproduced the issue with the uninstall that requires the original Exchange 2007 MSI but I don't know exactly why yet. Should know soon. I have the MSI log file and currently reading it. Pointing the uninstall UI to the original MSI will get you around this.
You will be able to install the newer rollup on top of the older Rollup 4. It will solve most of the uninstall issues. If you uninstall the newer Rollup 4 and then uninstall the older Rollup 4, you will still get into the same situation as described above.
M, I would uninstall the rollup. I am researching your problem and should have an answer. You do not have to do what I recommend of course. It just might save you some trouble later on if you have to handle an issue where you need to uninstall the rollup.