Have you tried silicon grease, not the thin stuff you get for door seals but silicon grease, they sell it a Q8. I smeared it all over the rubber seal and then use spray silicon where the seal joints the metal roof. Its messy but seems to work and can be cleaned up in the summer. Give it a go, it will do no harm, not cost a lot and be easier than patching the hole.
All the Best Michael
You do not own your Land Rover, you just maintain it for future generations.