It, I am sure, is also there to deal with the possible future constructions creating an internal corner; but the OP's garden boundary extends past the party wall.
The BOUNDARY rulemis ENTIRELY about building in the future. It's effect does obviously coincide with minimum CLEARANCE rules. Pluming and it's offensive effects are different, and actually don't have specific measurements. If there is a danger of affecting the neighbour, then you are at risk of enforcement action.
I don't meant to be offensive or patronising, and some may think I'm pedantic. But the above is my understanding and take on it, and if you write the wrong thing down, (even if it changes nothing) on a report, it could come back and bite you.
The OP has 600mm of garden between the party wall and the fence boundary, so even if his current or future neighbour built an extension, there would be 600mm of garden and rear wall between that the and proposed flue terminal.
You may well be right! I just can't visualise what the OP means. But he did say that a fence is nearer than 300mm, so if that is attached to his wall then he has a problem with internal corner rule.