For now I always thought of the targeting laser as a convenience. It made setting the focus much easier and helped placing the parts on material - especially if it is already pretty cut up.
But just yesterday I found out about a different way of using it. If you cut crooked material (typically plywood) the focus may be perfectly fine where you start cutting but may be off else where. With a bit of experience you can see that the focus is off even without the targeting laser. But you can not see so easily in which direction (although you might know from trying to place the sheet reasonably flat). I also did never try to change the height to refocus. Traditionally this requires putting an acrylic puck on the work piece and adjust the distance to the laser head. But the danger of accidentally moving the material around and messing up the part is much to high for this to be practical. But with the targeting laser you can just hit the <Pause> button, adjust the table height without even opening the door and then resume with the cut.
Yes, this is not feasible for a cut where the head moves between different areas a lot. But I often cut many smaller pieces and the head stays in an area cutting one pieces after the other. So this little trick can be used to improve the quality of the cut and to prevent parts not being fully cut through.