Well, this is just theoretical thinking and I can’t back any of this up, but since the 10.5” and 12.9” inch iPads Pro support fast charging (29W), it’s possible their Lightning ports are also able to provide more power to compatible products like the Apple Pencil than the standard 12W iPad charger. The fast charging is based on USB Power Delivery which I imagine can go either way.
If you have the 9.7” iPad Pro, though, then even this flimsy theory doesn’t apply since it doesn’t support USB-PD fast charging.
So I have an idea as to what may be going on. See on typical lighting cables, there are only one set of power terminals even though the cable is reversible. These +- contact points are wired together. This would be why a standard lightning cabled won’t fast charge the iPad, even with higher powered adapters.
With the usb-c to lightning cable and the apple pencil, I believe these + and - terminals on each side of the lightning cable are NOT connected. Instead, what is happening is that you have two concurrent power lines. The ipad has this same power output capability built into it’s lightning port (two separate + and - terminals). Since these devices carry multiple cells, what is happening is that each power line (1 on each side of lightning connector and port on ipad) is I/O’ing the maximum USB spec to each line, resulting in double the power.
I don’t know if that made any sense, but if it does, I believe that is what is going on.