Hey Ryan,
OK I think I know what you are talking about.
Generally you want the axes of the Thigh and the Shin to be the same. (for example Z axis pointing backwards).
And when you have multiple chains sitting on top of each other, like an FK set of leg bones and an IK set of leg bones, you want them all to be aligned the same way. This is something not shown in the course but imagine you want to switch from FK to IK using a custom bone property that turns on/off the relevant constraints to do just that.
The reason you want all the bones to be aligned is so they don’t twist awkwardly when you switch. (I hope that makes sense)
Now what’s happening in the video is that the IK constraint settings is trying to point the X axis towards the pole vector but the armature is setup in edit mode to have the -z point that way. So when you jump from edit mode to pose mode you can see the constraint jump. (I call this ‘mode shifting’ but I don’t know if it even has a name)
So if I change the offset of the of the IK settings to negative 90 that will aim the -z axis towards the vector target.
Then when you jump from edit mode to pose mode, the knee is still pointing in the correct direction.
Hope that helps.