I think maybe that might be something to worry about if the apple pencil becomes compatible across the entire iPad line, but with its Pro exclusivity one would have to have a pretty narrow scope in their design process to do that. Further, in its current, hopefully hobbled, state, tapping of targets remains the same, it's only the movement of elements that is effected. So even if apple were to permanently change the pencil to function the way it does in the 9.3 beta, poor design choices based on touch target size wouldn't be effected by this change in the pencil functionality.