Why do they use a flute to start their spaceship?
Are the notes played a reference to something else, or are they significant at all?
Here's a far flung, very unofficial theory that just occured to me: It could have been a tribute, a reference to the works of H.P. Lovecraft.
"[O]utside the ordered universe [is] that amorphous blight of nethermost confusion which blasphemes and bubbles at the center of all infinity—the boundless daemon sultan Azathoth, whose name no lips dare speak aloud, and who gnaws hungrily in inconceivable, unlighted chambers beyond time and space amidst the muffled, maddening beating of vile drums and the thin monotonous whine of accursed flutes."
Source: Wikipedia ("Azatoth" entry)
Okay, coming to think of how much influence Lovecraft's works are said to have on Scott's original Alien and the entire franchise, maybe it's not that far fetched. Remember, H.R. Giger's art book that Scott was given during the pre-production of Alien was called Necronomicon...
Ship is alive. That is the ultimate art of creation. Man can create material things, not live things, things that are assembled of other pieces, cut materials, welded materials.. A man work can never repair itself. But man can, man is a machine, an ultimate contraption where every single building block is alive.
"Engineers" were creating living nature, so the sound was the right frequency to communicate and thus activate the ship. That can be understood if one get to analyze the work of Thomas Campbell - My Big TOE.
Greek myths also have a message to us from old days, time when man was four dimensional being, when no language was needed to understand each others, to understand what our cells have to say, what they feel, what they need, what other creatures have to say each others, or to us, and now we think our technology of cellphones is remarkable...
Anyway, that is why Tesla didn't want to publish the radio communication, but discovering that was a nus-product of a bigger discovery, and always - naturally there are vultures like Marconi and Pupin.