Before humans used magic they had mystical powers from channeling spirits. These techniques were later strengthened by the introduction of preservation magic. And they merged to become Ritualism and eventually a part of the Guardian profession.
We are not entirely sure what the original abilities looked like. But a theme seems to be light/lightning. And now centuries later the commander is able to do a bunch of preservation-esque things with the help of the light dragon. All without ever being corrupted.
Beyond Crystal Champion/Aurene we have also bonded with the Raven Spirit. And light-like abilities comes up again.
I'm not sure how else to explain how we have magical protective powers from channeling bonds other than the commander is some sort of proto-ritualist.