TLDR: Add a button in CAT joints to select the bone it's parented to. Also makes it easy to unbind when you clear it.
CAT, with it being so outdated and buggy, is still a very nice animation tool just for the layers alone.
Here is a massive problem with it.... in a sea of other problems....
If you build a skeleton, lets say in AccuRig, and you want a CAT rig for it, the biggest pain for it are not all the rotation/position bugs, but it's parenting the CAT joints to the bones.
You can use Link, which is easy, but it breaks the hierarchy. What you need to do, is go for each bone and by one, and add Position and Orientation constrains instead their Lists. One by one!
And if you need to remove the constrains back to defaults, to do adjustment to the bones? You have to go through each bone, reset it back to Euler and hope it doesn't break, do adjustment, and then do the constraints again. It's ridiculously tedious and frustrating. If you dare to delete the CAT rig when you still have constrains, it just breaks everything.
Simple fix would be add a button to each CAT joint that selects the bone it controls, which essentially adds the Position and Orientation constrains in Position/Rotation lists. If you clear it then it uses default Euler XYZ.
There are still a ton of bugs with the bones and CAT but this would be a nice first step to improve it.