Does Magic Mouse automatically sync up with Windows in Boot Camp?

Once the wireless mouse is paired to the Mac, the mouse will work with Windows, the Mac Startup Manager, Mac Recovery, etc. Specific to your question, the Boot Camp Assistant restarts the Mac to boot the Microsoft Windows installer in such a way as to keep the mouse paired with the Mac. When installing Windows without the aid of the Boot Camp Assistant, often (but not always) a user has to plug in a wired mouse to install Windows and pair the wireless mouse after installation completes.

Unless you have installed Windows without the aid of the Boot Camp Assistant, you never realize how many steps are automatically done for you.