I had the stock kernel when I reflashed my ROM. All I didn't do was flash SuperSU because I need to be unrooted for Pokemon to work
Sent from my Nexus 5X using Tapatalk
on a side not if you want root and pokemon you could try
http://xdaforums.com/android/software/mod-magisk-v1-universal-systemless-t3432382
it hides root so safety net will pass. must use the superuser zip provided there and the app.