Nintendo's main franchises are all either openly in favour of sustaining a monarchy, even when it causes great unrest (Mario, Zelda), uncritical of monarchy to the point of monarchy and unintentional self-parody (Fire Emblen, pick any, say, Three Houses, Dimitri's self-centredness and lack of self awareness especially.), or feature a world where extraterritorial corporate land ownership is seen as the peaceful ideal (Animal Crossing).
I don't think a more extreme version of "enforce the status quo, by violence if necessary" is outside of their wheelhouse even for their casual games, while Three Houses (albeit obliquely) has several themes and events darker than Genealogy. I know people here, of all sites, would be aware Nintendo isn't just in the business of publishing family friendly faire, but a publisher who publishes across the spectrum from literal baby games (think Electroplancton) to what is essentially softcore with action elements (Bayonetta.).
They allow references (even acts) of genocide and child abuse in MARIO games (Origami King), I don't think a Fire Emblem having a standard-issue problematic plot is the biggest concern for them.