I don’t curently have free time to slate this for an update.
And I’m actually a little surprised it works on the new skeleton at all considering I did look at the skeleton and they made a real mess with lots of useless bones…
My 2c would be to animate and use the old skeleton, then retarget the animations to the new one instead of working directly on the new one.
I know it’s not as cool…
Also, consider that any professional animation has to be done on your final mesh to look good. So animating on the old mannequin is a stop gap at best.
As I get some spare time I will likely update this, but I have no idea when that will be at the moment.
(Sort of like any epic bug fix 
)