Edit Solution:
Right-Click Tools had a TakeOwn option. After using that I could look inside the folders (all empty) and delete them (select + delete key).
Ah, interesting. The Take ownership and get access option in Right-Click Tools uses the more powerful SetACL program. Good to know that worked in this case. By default, for your own protection, it wouldn't have allowed you to make that change on the WindowsApps on C: but a copy on D: is assumed to not be a system folder, so it will allow it.
I think it would have also worked to to go straight to the rd command in the Cmd here as TrustedInstaller prompt.