No.
It's fine if you have already installed versions of the separate routes and point the Ultimate Edition installer towards those to fetch the files it needs. As long as you end up with the correct files specified in the first post, the game should run. Where is your save data folder "faterealtanua_savedata" located (subfolder of the game folder, subfolder of user documents, subfolder of AppData)? If you're no sure which directory Ultimate Edition is using, you can check the file "config.ksc" in the game folder; it's basically a text file.