Yes, if you want the same baseline performance you're going to give up Instant Swap, and that's going to break the perfect mouse broadcasting. You can't have it both ways, sorry!

From the pdf:
One of the things the Quick Setup Wizard sets up is Instant Swap. What this feature does is sync the actual resolution of all of the game windows, such that even when shrunk, the windows are still rendering at the full resolution. This will somewhat reduce your framerate (FPS), but is required to enable Instant Swap and provide perfect mouse broadcasting. If you don't need Instant Swap or perfect mouse broadcasting, the same level of performance you had with Keyclone can be achieved by simply disabling this option in your Window Layout.