You're quite right. I've always taken it as the whole window (building opening) as that's what I was taught at college. I've just checked BS5440 and it's only the opening section of the window itself that counts - Good to know. A bit of a misunderstanding with terminology there, luckily I've never had to change my plan A on the basis of it. Every days a school day.
It does still look a bit close for the 150mm allowance for structural and temperature issues though. I know it's unlikely to cause any issues, especially with the flue temperature of modern boilers, but rules is rules.
It's the route of the kit that made me chuckle, it must have been a right pain cutting it through the gutter. At least it's not cast iron like the main roof gutter.