>>384543193
So I'm guessing the foot popping out was from the armature going back to its original shape and I had to some how change the shape back before applying the now rest pose. However the foot formation doesn't seem to be controlled by shapekeys in this case which is why I wasted so much time on it.
I am just gonna try to work around it by moving the meshes on Unity instead of Blender as I've spent enough hours on this.