Looking at this elevation view of the Falcon 9, the nozzle exit of the core engine in the cluster is in a different plane with respect to the nozzle exits of the surrounding eight engines.
Why is this? Is there an advantage to this layout?
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I think ForgeMonkey is onto something. I just ran across this article and thread, which includes speculation that the center engine gets some aerospike effect from the exhaust plumes of the surrounding engines, and maybe the vertical positioning of the nozzle is trying to optimize that.
Seems plausible, but I don't understand the fluid dynamics enough to say if that's really it.