Thanks for the feedback. As a leaseholder I believe I need to get permission from the housing authority to drill into the external wall, but I'm sure they can provide this at short notice given the circumstances.
Two engineers have now advised I should raise the boiler by 4cm (one has only seen the photos) while another engineer thinks the cap under the flue collar can simply be pushed down and screwed on (based on the photos below). These are very different solutions to the same problem.
I have also noticed there is a gap where the flue enters the wall, which can be seen on the first photo below. Is this safe?