These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Periphery Demographic: When the manga first came out, it was supposed to be aimed at elementary school girls, but the strong themes and religious symbolism was lost on them. According to the introduction on Fantagraphics' release, it was more appealing to older audiences, like young college aged men (sound familiar, bronies?), which saved the manga from drowning in the tsunamis of obscurity.
Values Dissonance: Juli's view of his abuse at Siegfried's hands as a "sin" for which he must atone can be jarring to modern readers. Possibly counts as Deliberate Values Dissonance, since this attitude isn't unrealistic for a student at a conservative, 1970's-era boarding school.