Yeah good point. It may be worth looking into cutting in an outlet in the center of the roof provided you can gain access from underneath and the soil/drainage pipe can run somewhere. failing that the correct way would be to strip the roof and decking and cut some firrings in to achieve the...
I couldn't help noticing that he has not covered the upstands to the wall with any lead he seems to have just pointed in the top of the felt which in time will leak.As for the pooling he could have flooded the roof with bitumen which would have levelled off the area and then felted on top of it