I used to do it with PES 2017 so I think it's possible. I had a PES 2017 "PTE" folder and a PES 2017 "vanilla" folder (both in steamapps\common and in Documents) and when I decided to play one or another I would rename the folders accordingly and then launch the game. I think that you could also automate the renaming process with a .bat file though, this would make things way easier. Downside: I had to use 2x the disk space a single PES 2017 folder would require (plus the space taken up by the additional CPK files of the PTE patch). But it worked, it definitely worked.