It is a reference to Noah's Ark but there's nothing about them being "The last of their kind" or specific reference to there being two of each person. There's a reference to Noah's Ark in the journey from the first period to the second as well.
--Basically I agree it's a reference to Noah's Ark but I don't know why we need an analysis on what it could mean for the story based on stuff that isn't supported by the text.
I say no on the shadow bit. We don't know enough of what Seth's logic was and there isn't enough supporting it to say for certain. This seems more like speculation--interesting, but mere speculation all the same. There could be many concepts he's drawing from on his advice.