Docking autopilot used to docks crafts parallel to eachother flawlessly and without intervention prior to some control change that was made in KSP 1.3 that MJ no longer handles entirely correctly.

In 1.1, this docking action was performed with the docking ports and control module in completely different orientations and positions: https://i.imgur.com/vmKxKJW.jpg

In 1.3 or later, if the docking port, and control module are not BOTH pointing through the CoM from the same axis, docking ships identical to the design above is not possible without a large amount of manual input, completely negating a large part of auto-dockings usefulness: https://gfycat.com/AmusingDisfiguredFowl

Log file from 1.3 attempt if needed: https://www.dropbox.com/s/leh4g3bkmb20w5x/KSP.log?dl=0

Looks like PID wobbles again, so probably fixed or lessened by setting the PID controller to HybridController and setting the MaxStoppingTime to 1 second or less.

Leaving this open as the video has a good use case to try to test.

So wait does this like partially work now, or still completely broken? Its one of the few things holding me back from playing ksp again tbh

I don't know, didn't replicate it yet.