Tree2: Pippin was my first Broadway musical ... I promise I have a very clear impression of it.
I do remember the elements you've mentioned, and i do of course recall them as dark (though the flying body parts i thought were played as a gag). so, sure, there's some dark there, but for lo these 3X years now my overall sense of the show has not been of darkness. the presence of dark elements does not necessarily translate into a dark story.
although you didn't mention it, i also fully appreciate that the main character spends much of the play deep in the throes of existential angst ... somehow, though, i don't think of the work itself as being existential.
moreover, on the slightly more pedantic side, i intended to question (or open up to question) the marketing department's assertion that the common understanding of the work is one of darkness and existentialism.
perhaps it's my (then) tender years combined with the wonderful melodies, but i've always thought of Pippin as one young man's journey toward finding himself.
"You, sir, are a moron." (PlayItAgain)