The way annotations / highlights are handled in the new iOS app with the Apple Pencil is great. If you want to delete an annotation, you de-select the Pencil icon and then you can change annotations (deleting, color etc.).
As the app does not make use of the Apple Pencil tap function, this could become even easier if by tapping on the Apple Pencil, the annotation icon is selected / de-selected. Maybe one can set the most recent used icon (highlight, underline, etc.) as the one to toggle with the Apple Pencil tap.