Your flat roof is already joined to the flank wall of his house. What is the difference?
Have you spoken to the original roofing company to see if they could do the necessary work to seal the new junction and include it in your original warranty? Obviously the work would be done at the neighbour's expense with their agreement.
Ultimately I suppose it would be possible for the neighbour to build his extension without sealing the gap to your roof but I think that would potentially lead to damp problems on your side.
There are two answers I could give you regarding the difference.
1. The roof has been there from day one and attached to his wall as part of an old shed from the home builds of 1949, so it's beyond our control and something that has to be accepted whether we like it or not. Him buying a home with those details listed on his home deed register and title plan means he has accepted that responsibility.
2. As you mentioned, the roof has joined his wall. Key phrase: "HIS WALL." I'm not stopping him from joining my wall, so he can join my wall with the appropriate party wall act and notices.
The roofing company point you bring up is a good suggestion and one I will take on board today. Though, given that his proposed plans show that the roof would be coming off my wall and his dropped wall, as my wall pushes out in front of his home slightly, it gives me the impression that the structure will be adapted accordingly. Therefore, he should adapt it to miss my roofing structure, with permission to attach to my wall only.
Regarding dampness, I believe that would be an issue for him, as my outer wall is exactly that—an external wall, which would then become his internal wall, I presume, or at least some form of prevention measures should be taken to ensure dampness is not a problem that penetrates through to my internal wall. He should seal off his roof at my wall, and guttering drainage should be installed properly. Otherwise, if not, I will get my surveyor back to assess the problems and abide by the PWA, and use property law should any of my property be damaged.
Because at that point, it would be obvious where the problem had started. If, for example, I agreed to his roof linking to mine and we had damp problems, then the burden of proof would be much harder, which is not a risk I am willing to take.
Simple: connect your roof to my wall along with your build, make the necessary seals and correct structural roofing methods to ensure no issues according to regulations, and happy days. He has already confirmed that he won't touch my roof and structural fascias. This could all be avoided by a simple flat roof, but who am I to suggest that to him? All in all, do not touch the roof and make good use of the wall.