Termination bar

OK, so I'm designing my own patio cover which will be attached to the house and have a metal roof. The house is stucco and I understand that the best way to flash this to the roof is to cut the stucco and insert a flashing under it. However, almost nobody around here (Albuquerque NM) does it that way, probably because our rainfall is so small. What they do around here is use some kind of endwall flashing and a termination bar with a bead of sealer at the top.
Unfortunately there is a canale (scupper canal) right in the place where the endwall flashing needs to go. I could drop the height to get below the canale but then the patio cover is too low. So, I would have to fit the endwall around the canale somehow. The canale is about 6" wide. I was thinking of just notching the endwall flashing to fit around the canale, then omit (discontinue) the termination bar at the canale.
What do you think? Got any ideas?
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Just to clarify, the picture is not my house but I posted it to show the type of canale I have. The canale on my house is actually metal, and the one in the photo looks like wood.