So I just re-read the entire series, and noted a few things, like a subtle retcon where the Sunflower Bookery was originally “in the middle” of the school grounds, then later “in front of” the school, a revision which makes more sense anyway.
Miss Sunflower & Onii-san’s family life: Both the mother and father worked a lot, and the mother walked out when Miss Sunflower was in grade school and the brother was in middle school. No real reason was given, although the father also seems to have been mostly physically and emotionally absent.
That left the two kids to take care of themselves to a large degree—Miss S. seems to have been in charge of meal prep and the household accounts at a young age, she rarely got new clothes, and she even celebrated her high school graduation with a different family (the couple who taught her how to run a bookstore). Onii-san moved out as soon as he graduated high school, indicating a lack of connection to the father, although later chapters suggest that it was about his grief at the death of the first Miss Sunflower.
Although the early depictions of the siblings’ family life suggested physical and emotional neglect, each parent got a bit of a rehab scene, in particular Miss Sunflower’s memory of her mother reading to her when she was sick. The father is shown as an almost compulsive reader, which still entails emotional distance and neglect, but reading is such a positive element in this series that he probably can’t be all bad.
The introduction of the first Miss Sunflower is where the series swings from being just a light SOL to something with greater emotional depth, and the development of how the older characters related to her and how she parallels and contrasts with the present-time events makes her the thematic pivot of the series—characters are always thinking of how others are or are not like the first Miss Sunflower.
And it’s almost (but not quite) not a joke to say that in certain respects this is the most offbeat harem manga ever, as shown by Miss Sunflower at the beach surrounded by her young worshippers.