Okay, So I'm 90% sure I know the answer, however I'm not the best to explain it as I only know the song and game from osu! and a walkthrough I watched once. So bear with me here.
Although it can be scary,
Everything ends alright.
At least it did for me,
But that might not be right.
What this screams to me, is that this 'thing' is both a Horror game, with things that impact whether the ending will be a good one or a bad one. Ib fits that Mold.
Choices make all the difference,
Don't take any lightly.
Everything changes how it ends,
Abruptly or quite nicely.
This fuels my first point some. Think about it, RPG maker games mainly focus around the user having to make choices that determine the outcome (Mogeko Castle is a fine example, A messed up, but fine example). As well as Ib. Some endings turn out good, some endings do not.
This could be a hint at the use of the keys AEABCDEABE (Thanks, DooplissForce. couldn't have got that without'ya) with some of the keys ending flat, or sharp.
Edit: I forgot to mention, that the tune from the whole thing, sound a lot like a part of this tune here: Ib "Memory"
Now onto my main reasoning for my thoughts to it being this!
Be sure to check out all the paintings,
Each one could fell even the mighty.
PAINTINGS! paintings, paintings paintings paintings.
What's one of Ib's underlying features? the use of paintings to fuel the storyline. For example The whole thing is held in an art gallery. A quote from the Wiki - "A young girl named Ib visits an art gallery with her parents. While observing the many exhibits, she suddenly realizes she is alone. And in her search for others, she finds things awry in the gallery..."
The whole games premise is based around the paintings and defeating your enemies with the use of them, as well as other things in the game.
In fact, two of the endings from the game are titled Forgotten Portrait as well as A Painting's Demise
Any help toward my point would be great. If you have something I missed, please let me know in the comments.