I drive my Miata like my Ducati Superbike.
I run 50N rear springs with 12mm of preload (and almost all of the rebound damping the rear shocks have). I get little bottoming, probably none. I did this because I DID get a lot of strikes on the bumpstops and it really upset the car on one of the on-ramps I use every few days. It also lets me run ~13.75" ride height that further reduces bottoming because I have more compression travel. The stiffer springs did not change the ride comfort, that I can remember (it's been about 8 years), other than stopping the harsh jolt when the suspension ran out of travel.
Were I you, and I had 40 Newton, stock, springs, I'd set the preload at 15mm and adjust the ride height back to what ever you like. If you have the Sport Suspension option, you may want to switch the the 11mm base suspension rear stabilizer bar. Or, maybe switch the smallest RX-8 front bar.
'06 Sport 6MT Ohlins 70N/50N