This bit made my spidey Murata senses tingle:
私は姉とも両親とも似ていないが、なぜか由宇にはそっくりだとよく皆から言われるのだった。
There must be an actual, real-life reason why both Natsuki and Yuu feel like they don’t belong in their families. It’s like they’re subconsciously picking up on subtle cues (e.g. Yuu’s mother telling him to call her by her first name, Natsuki’s mother openly favouring the older sister and putting down Natsuki), but for want of knowing the truth they have concocted a fantasy narrative to explain these feelings 
Also, is it just me or are there some warning signs that Yuu is being abused? For a start, there is Natsuki noticing he seemed to have become smaller over the past year, but also the way he seems to be parentified/spousified by his mother(?):
由宇はおばさんのことを名前でよぶ。美津子さんが、そのほうがいいと言っているそうだ。美津子おばさんは父の一番下の妹で、三年前に離婚してから、由宇に恋人のように甘えるようになった。寝る前は毎日美津子さんの頰にキスをしなくてはいけない、と由宇が言うので、「本当のキスは私としてね」と約束していた。
After some wikipedia’ing I also wonder if this might be some ominous foreshadowing, though perhaps that’s a bit of a stretch.
蚕から糸をとったんだよ、と教えてもらったが、糸をどんなふうにとるのか、それから蚕がどうなるのかは聞きそびれたままだ。
Also, this bit entertained me:
お手伝いができる年齢になった女の子たちは皆、台所へ行って夕飯の準備に参加する。
It seems to be almost universal that when there’s a big family gathering, the women do all the cooking and the men never see the inside of the kitchen (but do get served first!) 
As for the bit that gave me the most trouble… お盆にのせて運ぶ。I was so used to it being Obon, that it took me way too long to realise this was about trays lol.
