No. It is still the same save, but you don't have to install the game again. This mod uses its own launcher which creates a virtual mod directory in your game folder and generates a chunk file for that. This directory is a symbolic link and will be removed when you close the game (as long as you keep the launcher open in background). It is just like the Nexus launcher for Skyrim and based on my Simple Mod Manager tools. Even the chunk cache will be reset after closing the game. That means you don't have to copy any files to your game. It stays completely clean.
There is an exception.. Trons and sound files will be overwritten, because this aren't controlled via chunk cache. But the launcher creates a backup from this files and also from your save game. It does export all your pofos, movesets, teams.. But for now there is no option to restore the backup. A separate uninstaller will be available with version 1.1. Handling with the save game is too dangerous, because it could possibly break the game. So it just backups what it has changed.