I have now reconstructed it all and found the entire fix, thanks to the assistance of my software engineer and Claude.
The latest versions of Nisus Writer Pro (I have 3.4.1) are Universal, not Intel, and run natively on Apple Silicon. It does not need Rosetta.
Apple's own System Information.app tells us so. The Activity Monitor tells us so.
The thing that triggers our Macs warnings about Intel support is an app bundled with NWP, the Nisus File Converter.app (Applications>Nisus Writer Pro>Contents>MacOs: in this folder are found two separate apps: Nisus Writer Pro.app and Nisus File Converter.app). They also run separately, and if you search for it in Activity Monitor, it shows you that Nisus File Converter.app is Intel, a Libre Office pre-Silicon app.
Now, people have deleted this app from the bundle (it is just used to convert files to import in NWP, and the standalone new Libre Office does as good or even better job). And it does not break NWP in any way, and the warnings cease.
But there is a snag, if minor. The app is listed in the Code Signature of NWP. As NWP is an old trusted app, MacOS may never decide to check its code signature -- but if for any reason it does, or if you move to a new Mac, there is a good chance that it will shut it down because it does not pass muster. One can reseal the NWP if MacOS objects to it but is is a procedure somewhat iffy and may need frequent repetitions.
The better option, offered by my experts, is to deactivate this app in NWP settings:
open Settings ▸ Advanced.
Untick "Load file importers in the background after Nisus Writer starts".
Set each of the three importers to Apple's own rather than LibreOffice.
This worked for me. The warnings stopped. NWP runs without a peep. And there is the near certainty that this app, which will become incapable of functioning after Intel dies, will not impact the functioning of NWP at all with its corpse, except for what concerns importing files like .docx with well preserved formatting, which Apple does not do well and Libre Office does much better.