Thanks for posting the pictures.
Just a thought is the pilot be extinguished by the wind coming in or the exhaust not being completely vented.
Here's a picture of our previous Sunline T-2670, but this was an auto-ignition HW unit.
For a simple test / adjustment, you may want try bending the flange a little more to decrease the opening (or increasing the opening). This may help with exhausting to see if this may be the problem. It would be a simple mod & test before going through the effort of attaching additional sheet metal.
If that doesn't work, maybe you could add a wind deflector on the inside of the door, on the bottom of the door vent. Not sure if this is what you were originally thinking of doing.
We're bringing our Sunline home this evening to get it ready to go to the Eastern M&G, so Iíll check it and compare to your picture.