On the flip side, how could I prove that someone planning a twenty story skyscraper is doing so on a conscious level, utilizing a higher intelligence?
Whether or not everybody in the same species does it.
Doesn't that seem to be the distinguishing feature? If something is an inherited instinct, then every member of the species (or most, at least) will inherit the instinct and you'll observe the behavior. Most beavers get into dam-building, right? We can probably assume therefore that beaver dams aren't the individual inventions of individual beavers, but something they instinctively do.
Similarly, if almost all humans felt compelled to build twenty-story skyscrapers, I think we could assume that was instinct. Instead it seems to be the province of a relatively small number of architects.