If you're done with one, you can just delete the folder, and it will do no harm to the rest of your installs.
You can install different versions or configurations of Reaper, and they do not bother each other (and do not bother a regular Reaper install).
If you install Reaper with the 'portable install' option selected, it places the entire program and associated configuration, themes, hotkey settings, license, etc, into a single directory (as opposed to the traditional method of installation, which is not fully self-contained.)