Non uniform transforms generated by the ik constraint cannot be used by blender operators: Apply visual transform to pose, Animation bake, Copy Attribute, FK/IK snap, none of them will work
Exact steps for others to reproduce the error
Attached blend file contains a very simple ik setup, and a copy with a baked animation, which behaves different. Baking the animation, applying to pose, storing the matrices and setting them, will not end up with the same pose.
This happens since non uniform scale IK has been introduced, and it's fixed disabling USE_NONUNIFORM_SCALE at build time