Lumen always this ‘creeping noise’ in the shadows. I think it will be quite a while before that goes…
You know that ‘everything looks like a nail to the guy with the hammer’ thing? That’s Nanite. Don’t use it if you don’t need it.
Like I say, Nanite works on a PER MESH basis 
Your meshes are not complex - boom - you don’t need Nanite.
Try the same experiment with 500,000 insanely details statues of the Buddha, and use Nanite instead of instancing, and that work work.