So, I made the change to "kvariant", and installed the kernel, but something broke and I had to manually restore the /boot partition with files from another Pi.
If anyone needs to fix his install,  I recommend to
yum reinstall raspberrypi2-kernel-firmware raspberrypi2-firmware
and
yum reinstall raspberrypi2-kernel-4.9.64

Another thing I noticed is that the config.txt supplied by the CenOS distro sets
arm_freq=700
This is disasterous if you are running an RPI3 :)  Here is the setup I'm using for my little RPI3 Samba Domain controllers:
---

hdmi_safe=1

#overclock rpi3 moderately
#https://github.com/retropie/retropie-setup/wiki/Overclocking
total_mem=1024
arm_freq=1300
gpu_freq=500
core_freq=500
sdram_freq=500
sdram_schmoo=0x02000020
over_voltage=2
sdram_over_voltage=2

#minimum video ram
gpu_mem=16

#disable wifi and bluetooth
dtoverlay=pi3-disable-wifi
dtoverlay=pi3-disable-bt

#fast sd card, only for UHS cards 
#(may prevent booting, have tools on hand to revert this)
#dtparam=sd_overclock=100
#boot_delay=2



--
Kv,
Kristján Valur Jónsson, RVX