A game i recently completed, Stella Glow (great game btw), is is a similar category to these types of games, niche and likely to turn away anyone who finds "anime" games weird. It has everything this game has had removed so far, panty shots, fairly underaged girls, boobs and lots of fanservice beyond your wildest imagination. Yes, it's localized by Atlus, not Nintendo, but by your logic it should have had all of what i listed above removed because it can be played on a Nintendo 3ds, a family friendly console.
Parents and the like would not let they're kids buy these kinds of games if they don't want their kids exposed to the themes found in niche japanese, fanservice filled games. TMS #FE isn't going to be bought by kids or younger teens who are probably supervised by their parents/guardians, the game wasn't made with that audience in mind. So why censor it, i still fail to see any logic behind it, and probably never will because NOA is horrendously terrible with communicating with their consumers.