The Scythe Ninja 5 might be a quieter cpu cooler.
Test results with the fans running on maximum (12V) and 130W cpu-simulator from hardware.info:
Dark Rock Pro 4 - 49,2 °C - 41,8 dB(A)
Ninja 5 - 53,1 °C - 30,4 dB(A)
When I tried adding a CPU cooler (air) it was added in the bottom right corner instead of above the motherboard. It would also be nice if it was possible to adjust the height of it.
Simple and cheap, similar to Jonsbo C2
SFX PSU
Under 10 liter
Top IO: power button, 2x usb-c and 3.5 mm
140 mm case fan
Magnetic dust filter
Bottom to top airflow
Easy access to both sides of motherboard (maybe with a slide mechanism similar to DeskMini A300?)
The smallest mATX I know of is the (Cooltek) Jonsbo C2 with volume of 12.10 liter.
http://www.cooltek.de/en/jonsbo/c-series/126/c2
http://www.jonsbo.eu/en/c-series/43/c2-black
I had some mATX motherboards (or was it the GPU) that didn't fit and put those in the bigger 18.82 liter Coolcube Maxi...