When using the pencil via Cmd-click, in Logic, you are in any case changing tool. The only difference with the method used in Dorico is that in Logic you are in latch mode, in Dorico in toggle mode.
An advantage I see in the Dorico way, is that you can switch between various different tools, without having to reassign them to the Cmd-click shortcut. I very often wish to be able to quickly switch between Select, Pencil, Scissors, and Line. Unfortunately, with Logic you can only switch between two tools.
Paolo