Hi, thanks for sharing this issue.
The problem here is that the PackageReferences are resolved during the package resolution step, which is performed and controlled by VS, where NCrunch has no chance to introduce alternative logic.
The package restore step creates the project.assets.json file with the physical bindings to your package. To my knowledge, it isn't possible to introduce conditional logic inside this .json file .. and if you could, VS would wipe it out anyway the next time it restores packages.
The best approach here may be to examine the package to see if it provides any opportunity for disabling its build steps under NCrunch. Does the package have a property of some kind that you could inject to override it or disable it?