As the system is designed to emulate a pen-and-paper style of interaction, there is a good match with the real world. From comments made by participants in the user testing, the choice of this pen-and-paper metaphor was well received.
The action of scribbling over strokes in modify stroke groups is similar to scribbling over a mistake. Similarities like these can cause confusion because the result of the action is not what one intuitively expects for the metaphor of pen-and-paper. Of the people who used the system, none of them found this confusing.