Aligning CAT rig over another skeleton

I’m trying to align a CAT rig (Max2011) over a point helper skeleton with maxscript but I’m getting some weird results…

Doing CATHub001.transform = b_Hips.transform works, but that’s all. Doing the same with the spine works only for the position of the first spine bone of the CAT rig. And checking the rotation matrix they are indeed different. On the other hand, using the align tool from Max interface works, and the rotation matrices then are equal.

Another weird thing happens with the foot. Doing CATRigLLegAnkle.transform = b_LeftFoot.transform aligns the “front”, sub-object, pivot, whereas using the Align tool it aligns the “ankle” pivot, which is just visual. The links are some screens for the results.

I know I would need to do the align in a certain order (the IK extremes first, foot and hand, then arm and legs), but that comes later, after I’ve figured out how to get the skeleton transformations onto the CATrig. I could do it manually, but I would really really prefer to have this automated so the process of attaching an animatable rig over the game one becomes much faster. Are these issues because CAT use proprietary controllers? And if so, is there a way around it?