This is apples and oranges, though, because of duration. A song is typically a few minutes; a sculpture or painting is one image. There are many poems and short stories that are simply happy and beautiful. The brevity means it's okay to just have the one thing. But if, for instance, the music is taking the form of an opera or musical, then there's some type of conflict, even in the comedic ones. It's not so much about negativity as it is about being realistic about change: Nothing stays static, the one constant is change. Now if something is short, then change doesn't need to be included, but if something is longer, then it has to be. Or the static element will eventually get old. There's a reason we don't just play our favorite song on loop or just eat our favorite food endlessly and to the exclusion of any other.
I'm an atheist too, and quite happy in my atheism, completely fine with the idea that this life on earth is all that there is. And I never took this show to be a metaphor; I accepted it as an exploration of (the show's concept of) an afterlife. But I was very interested throughout the series and loved the finale even though I don't think it's what actually happens after we die. I mean, if one takes it broadly enough, pretty much any fiction could be said to be pointless because none of the characters are real, the story didn't really happen, it's set in a world that doesn't exist, or things happen that aren't possible in the real world.
My own personal take was that Jason, Chidi and Eleanor ultimately felt sated, rather than suicidal. They were ready for the next thing, which was not ceasing to exist, but becoming part of the greater universe, like a wave's water going back into the ocean. Eleanor changing into sparks of light will remain with me for a long time.