I guess by now, everyone kinda agrees that the point of "Matryoshka" is that is doesn't have a point. The seemingly random combination of numbers that is 524 in the song is the first five numbers except for one and three. An alternative reading for one is "i", whereas three can be read as "mi". Thus, the song is missing "imi" - in other words: meaning (意味).
Keeping that in mind, the song seemingly still calls out to someone because Miku/Gumi can't understand certain things and seek some greater meaning within insignificant details or that they simply are lagging behind in terms of knowledge which is why there are so many apparently pointless questions asked throughout the song. However, they decide not to care at all because no-one cares about them. Thus, they end up doing their own thing and sing and dance however they want to, considering themselves a messed-up, crazy patchwork of matryoshkas; but at the same time, they don't want to be left all alone either, begging to not be left by everyone else.
The matryoshka motif, though, is actually kind of interesting - while there is no meaning on the outside, the deeper you dig and the more you think about the song, the more conflicting and, well, deep it gets. It's a tough one to try to understand, but in the end, it's just nonsensical, anyways.