You should surely be able to just solo-defeat the FX-channel, no?
There are far worse problems with iZotope RX’ integration with Nuendo. iZotope gave up on trying to fix those issues, which is garbage seeing that they marketed a certain functionality which they now abandoned. I would bet my money on Nuendo’s relatively poor windows management as being part of the problem, with the way it locks out access to the main app when an offline process window is open as well as what happens when switching apps in terms of window focus. In other words I’m guessing iZotope gave up because Steinberg did nothing to help, and of course the threads already started on this yielded zero response from Steinberg, which is par for the course.