See if this helps. I think when you say "pencil tool" you mean the Draw tool (i.e., not the pencil icon that shows up with the Smart tool). It is confusing that the Draw tool and the Smart Tool in pencil mode have the same icon because they do not work the same way.
I'm pretty sure if you start drawing with the Draw tool (i.e., click and drag), you'll draw nodes. This tool is for drawing and creating freehand or periodic automation shapes. The Smart tool in pencil mode is for entering nodes for the purpose of doing "rubber band" automation changes, where changing the node position changes the position of the lines that define the automation. You can't draw freehand with the Smart tool in pencil mode, and you can't do rubber band automation with the Draw tool in freehand draw mode.
You could try a feature request that the Draw tool also be able to create individual nodes, but I don't know how difficult or easy it would be for one tool to cross over into the functionality of a different tool. That's a Noel question.
BTW - I rolled back to Gloucester to see if there was some kind of recent change, but Gloucester behaved the same way.