The benefits of proper flashing will be apparent on shingle roofs where the water can run out on the the shingle below the flashing.

On rolled roofs, this benefit is not available and the water will run down the channel that is provided by the flashing. While it runs down the channel, it's free to spread out toward the roof and the flashing would need to be quite wide to prevent it from reaching the deck. This is generally why flat roofs inevitably leak over time. The flashing is just not up to the task.

I also agree that a proper torch down roof would solve this problem. The torch down can be bent up 90 degrees onto the block wall and no water penetration is possible in the joint. To assist with this 90 degree bend, you might ask the contractor to rip a 2 x 4 with a 45 degree angle on the face. This would allow the torch down a transition zone and give it some longevity at the radius of the turn. The contractor will negate this idea and tell you that you don't need it. He's correct if you just want to make the 5 year warranty.