"Ok, So there are probably several techniques then.
I always though that the flashing was supposed to stay above the shingles to prevent water infiltration under the upper shingles."

Yes, to prevent water from getting under the shingles the flashing must always be on top of the shingles.
If you will look closely you can see that the flashing is on top of the 2nd row of shingles, the 1st row covers (or hides) the flashing.

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Rick Cantrell
Columbus GA