Ok, I see what you mean now. I'm guessing its handier for the roofer to just add something new rather than looking in detail at what is already there.
He said that if all the discharge from the top dormer roof was coming down a new drainpipe its very unlikely the leak we were seeing would recur which makes sense based on what we have seen. Nevertheless it would be good to find and resolve the source of the leak.
What I don't understand is if gluing an aluminium flashing to fibreglass to form a new outlet is a good (or long term) solution or if something else would make more sense.