I'm testing this solution( disable auto-strut before docking) just now. Here are some results.
1) The root change is not completely random. It has something to do with the craft type and how many auto-strut parts each craft has. It seems the "Plane" type has higher root priority over the "Ship" type and the "Ship" is higher than the "Probe". If two craft share the same type, the game will compare which craft holds more auto-strut parts and shift the other ship's root to it. It's quite reasonable, considering this approach can minimize the "changing impact".
2) Base on above fact, there are no need to disable all auto-struts on both crafts before docking. Instead, you need to change the craft type by re-name it and disable all auto-struts on the ship which is not going to be your new root. This gives your more control of the root changing.
3) Un-dock will restore each crafts' original roots.
5) Combining use of different types of auto-strut can be a disaster due to the re-calculating. Using auto-strut to root only.
I think we can end this discussion here. Thanks for all your help.
