"bottlenecks" arent specifically for exhausts pipes only. just think of bottlenecks as things that interupt the smooth flow of something.

for example. modding your car with an aftermarket intake and 2.5" exhaust and a free flowing muffler on the integra. then you go ahead and add some lumpy cams. the bottle neck will be the part that interupts that flow, which would be the header.