First, OneDrive only moves libraries if you enable backup for that library, something that the user is prompted to approve during OOBE or when setting up OneDrive.

Thing is, library locations are an environment variable. This isn’t a OneDrive issue, using an absolute path is bad software development. The issue you describe is not unique to OneDrive, it also affected users who had remapped their libraries to a secondary drive or literally anywhere other than C:\Users\Username Ironically, the original Oblivion release respects the environment variable path. The same is true for virtually every other piece of software, which is why so many users were confused encountering this for the first time.

Most Shortcuts default to C:\Users\Public\Desktop which is not indexed by OneDrive, but user created shortcuts or those for apps that install to the user account’s AppData folder (Discord, Zoom) will end up on the regular desktop. For those who do want to back up their desktop but don’t want machine specific shortcuts showing up ‘dead’ on other machines, you can created a shortcuts to the Public Desktop that the user can drop their other shortcuts into.