I think the best OS for Natami would be AmigaOS3.9 + Boing Bags 1, 2, 3, 4, ........ Plus any needed software patches from the Natami team to provide support for their SuperAGA extension and higher quality audio.
Natami is a very interesting idea that should have happened 15 years ago, but couldn't have because the tech (needed large, relatively cheap FPGA's) was not available then.