The Quads are only 16bit which will limit the minmal possible steprate. Adjusting the prescaler on the fly would help but I'm afraid that this will open another can of worms. I'll stick with the PITs for the main timer and use the TMRs instead of...
I'm currently working on a project which will include some steppers. Thus, chances are good that I need to get TeensyStep working with a T4 anyway. I can't promise anything but I'll try. As you already mentioned: don't expect better performance...