After Effects can save Preferences of Interface Workspace in Project? As with locking panels (Lock Toggle Viewer), for example:
So when I reopen the project, even after I resetting the Workspace, the panels back to the way were when the project has been saved for the last time.
in Red some examples of changes that I want to preserve in Project, independently.
No, that's not possible. AE only stores a reference to an existing workspace in the project, but not the actual layout and it never stores info on multiple effects panels and al lthat even if they are locked.