i don't see the letter at the end like an explanation, but in there there's something i really liked: when she said that she don't want gaku to read that, but she want gaku to read the letter.
in life there are a lot of normal things that exclude others, and you can have one or the other,
if you want both, you have to wait the life after life some religions believe, or you need to make do with dreams or sci-fi.
and it's coherent that there isn't a real explanation to the abilities of the purple-eyes persons, they are so absurd (not even in bleach there are abilities like those) that every possible reason would ruin all the story (the apple and the screw were beatifull),
the meaning that i, personally, see in this story is that there are things that you can only accept, and if you can't, you need to have faith, and not in some gods, but in people.
however, after reading the long awaited last ch. of saki, i realized for the first time : gaku X marii = hisa X mihoko