Why did you copy and flipped the bones instead of using the head/tail slider in the copyrotation constraint ?

This would be my question, too, since this slider already existed in Blender 2.66.1:

Setting the slider to "1" makes the "Constrained Bone" snap to the "Tail" of the "Constraining Bone" instead of its "Head" (slider set to "0").

I've found the answer to the question:

At 34:18 following in the video, Kent renames the duplicated and flipped bones of the "Toe Root Bones" into original "Deformation Bones" (they are already named as "DEF" but need their index ".001" to be removed) after having renamed the original "Toe Root Bones" as "Control Bones"