Sorry for the necroposting.
I’ve had the same problem, it’s pretty much impossible to use Dragonfly to dock a module to another vessel because of the CoG problem. But, I tried something last week and this week - PursuitMFD. It works wonderfully well with off center maneuvering.
I opened for editing the Station Building scenario with a cube and adding cylinder modules so I have four. Ran the scenario, launching the Shuttle-A from Habana to rendezvous with the Dragonfly. Used the Dragonfly to catch modules one at a time docking them to the shuttle using Pursuit and it worked great. It brought each one in docked keeping orientation spot on, just set Pursuit on DF to Z10 to bring the free dock of the Module nose to nose with the target dock. So my assembly was the cube docked to the Shuttle, the four cylinders to the cube up, down, left, right, then the DF opposite the Shuttle. That way, the shuttle’s Z-axis is balanced. Then I plane-changed, and rendezvous with the ISS using the Shuttle. Dragonfly was able to move each cylinder to dock 5 in series, lastly the cube at the end, finally docking the Shuttle and Dragonfly to the cube.
The hard part was to select which dock on the modules. Used DockMFD with the target selecting each dock in succession and look for the ranging rectangles until I see the dock I want, then selecting that dock in Pursuit.
Pursuit did a great job in all this process, with no issue with the off center thing.
Next run I’ll try the modules connect in series to see if the CoG really out far if it causes Pursuit to hiccup.