The iconic notes are the base, sort of a cryto-key for the rest of the language, which explains why the mothership takes control of the keyboardist and just starts spouting out notes.
The scientists and keyboardist mention they have no idea what they and the ship are actually "saying" to each other but it arguably doesn't matter. Just the fact that humanity recognized the notes as a form of communication and responded in kind is enough to prove to the mothership humanity is intelligent enough to establish some form of relations with even if it will likely take years if not decades to actually learn enough of the language to properly communicate.
Some of those people returned by the aliens were abducted in the 1950s and before. While they were experiencing God-knows-what in what was likely a relatively short time, all their loved ones, relatives and friends back on Earth, who've probably been searching for them, either have now aged radically or died. They also now have to reorient themselves to a new era with new trends, new values, and technology which may or may not go too well.
