Tar Monkey, here in Texas we almost never get copper.
In this sort of situation, what we do is simply pop the nails, pull out old shingles & then slide in new ones. If the production used staples, then we can reuse one of the two holes poked in the flashing because the nail is larger than the factory hole.
If it’s nails, then we need a new penetration point & the old nail hole is siliconed over.
As for your question with the arrow, I will need to see that section up close however I think it was masoned in with step flashing on the corner.
I’ll also respond to Horn1 on HornFans which is where he also posted the same question.
Horn1, if you’re in the Central Texas area, send me a PM via HornFans & I can do an onsite inspection to tell you where the production build went wrong on the roof (happens all the time with mass production roofs).
RanchHandRoofing / NCAAFBALLROX