It's a metaphor for a metaphor.
If the bottleneck is the part of the bottle that's the narrowest, then in a production setting like a factory, it refers to the stage or element of a system that limits the output.
Like traffic on an on-ramp, unable to flow onto the highway, the inputs get backed up. No matter how much you increase production in other areas of the system, the throughput (and ultimate productivity) will be limited by that bottleneck.
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