Does a Skylight need to be installed with the dedicated flashing system
I just searched for a kit and it looks like the one you have picture is by Velux, and it illustrates it on the same roof you plan to use. Perhaps that is the way to go.
It may tell you this in the instructions for the flashing install, but on the piece below the skylight, I would flatten out the standing ribs just a bit to help ease the membrane over the top of the lower piece. That way no sharp corner could pierce the membrane.