I use the same script for all Unity games for Windows:
Do you generally get Unity games running with a good framerate?
Yeah, normally they run about as well as they would on Windows.
Unfortunately, I use a bunch of Windows API calls
What for? Windowing, I/O, audio playback, and rendering context would all be wrapped by Unity wouldn’t they? The only remaining thing I normally use OS calls for is hot-loading DLLs.