Nuendo doesn’t save certain very project-specific things on a per-project basis. A couple examples:
The divided track list. The size of it will carry over from the last project you opened.
Custom quantize settings carry over from the last project.
And certain others that are almost always unique to each project. These kinds of things are important to maintain as unique to each project, in my experience. Or if some reason you like to re-adjust them again when you open up each different project, make it option.