No, you will need to keep the duplicated folders as they are or the solutions will not work without hand editing each file to change the path it is looking for the helper files. 
I created a folder called 'pmessenger' and uploaded all folders and files into it. When I navigate to the folder, the setup launches and the initial diagnostics are passed.
There is a file path error, however, on the next step (license verification). I receive the error pasted below.
Framework file not found: ../../../../../pmessenger/Templates/install.dwt.php


