USB C with custom Arduino M0

Why not, it's an upcoming standard. So for new products it will be good to explore. Apart from that they are available as being splash proof and much more rugged than the current micro-usb connectors, also nice that one can integrate them into the pcb so that they form more or less an integral part with the pcb itself.
Ah and I forgot the most important reason: some people are clumsy enough to molest micro-USB connectors whilst reversing the cable (believe me it happens).

I mainly struggle with the crossed D+ / D- connections on the PCB. It seems that it is too narrow to fit a via (0.3048 / 0.508 mm) in between without getting too close to other pins.