Flashing should overlap the roof-covering material, but on asphalt shingle roofs, for aesthetic reasons, the part of the headwall flashing that extends down over asphalt shingles is often covered with a course of shingle tabs.
No minimum headwall flashing dimensions are provided that are applicable to every manufacturer and jurisdiction, so you’re only concerned with seeing that headwall flashing is installed in a manner that will keep the water out. Common flange sizes are 4 inches by 5 inches. Headwall flashing typically comes bent to 120° and can be fairly easily flattened for roofs with shallower pitches.
Occasionally, you’ll see a roof which has had 90°-sidewall flashing installed as headwall flashing. These don’t bend well to accommodate roofs with steeper pitches, and you’ll often see gaps beneath the flashing. Wind-driven rain can enter at these gaps, causing roof leaks.