On a plunge cut, the scribe marks on the face of the blade cover (I show these in the manual, as you noticed) are intended to represent the start and stop locations with a full blade depth. Generally speaking, you do want your depth set to maximum. If there are times when you do not want the depth set to maximum, then yes, you will need to create your own Start and Stop scribe marks. The other poster’s suggestion of putting tape on the face of the saw for these marks is excellent. The position of these marks will vary with blade depths, so that is why the permanent marks are only for maximum blade depth.
One thing to note about a plunging cut that is different from a non-plunging cut, is that you will have tearout at the underside-rear of the cut. This is because this is the only time the rear of the blade (downward traveling teeth) are cutting virgin material. In a normal cut, the upward traveling teeth are the ones cutting virgin material, and tearout is mitigated by the splinterguard(s).
To reduce this particular underside tearout, you will have to employ one of the many alternatives, such as a backer-board under the cut, tape, or even flipping the saw around with a deeper depth to trim the beginning of the previously shallow cut (i.e. plunge at shallow depth, then finish at full depth, then spin the saw around and trim the beginning at full depth). The best method depends on the conditions and setup for the task.