Actually, I don't have the Unity plugin installed yet, as it only became compatible for Unity 2020.1+ just a few days ago. Also, I didn't delete the files from Windows Explorer. I deleted them while inside the Unity environment, so that Unity can track the changes properly.
In any case, your suggestion to disable the "Find moved and renamed files and directories" worked! After disabling, Plastic added the 3 files to the "Deleted items" category, along with their respective .meta files, which is actually the expected behavior.
Thank again!!!