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I know this is a dumb question for me to ask, but does VDesktop place itself in any folder other than the “pi” folder? I already know that it also appears in /media/pi, after uninstalling Pi Power Tools.

[Botspot]

but does VDesktop place itself in any folder other than the “pi” folder? I already know that it also appears in /media/pi, after uninstalling Pi Power Tools.

In your host system? No.
By the way, /media/pi/vdesktop is the mount point it uses. This special folder does not actually take up space on your system, but instead it behaves as a type of "portal" to another filesystem. While vdesktop is booting an .img, you will notice that /media/pi/vdesktop is filled with many files. But those files are really being stored inside the image. /media/pi/vdesktop is just a portal to allow you to see inside the image like that.