When you get to the final level of Eversion, you have to change the level from dark red evil to bright blue good and happy in order to get all the gems. But, in order to get some of the gems, thus the final level and "good" ending, you have to go all the way back to the dark red and evil. This shows how the "good" ending is not truly as good as it would seem, at least on the first playthrough. Possibly not intentional, but still mildly interesting.
One of the Fission Mailed screens is "Behind you". It seems like another attempt to invoke Paranoia Fuel, but considering that the first level you encounter this screen is World 6-X, which features a wall of blood moving towards you, this makes sense.
The first pit you ever ever jumped over is large enough to contain one of those movey killy hands. Aren't you glad you started out in X-1?
Also, once you see what the jewels look like in X-7, you may realize that you've been knocking the face blocks' skulls out of their heads.
Actually pretty funny if you think about it, as the face blocks don't flatten or anything.
World X-4, the fact the that the monsters stop moving is bad enough, but in an ending from the HD version, both Nehema and Zee Tee are stuck at their locations for all eternity.
The game has a 9th layer that isn't ever used. It changes the enemies into Zee Tee, which is actually more of a Mind Screw for the implications about what they and Zee Tee himself truly are and the righteousness of killing them.
What does it mean?! Unless... oh, no. You Are The Demons. More specifically, the Asterisks are just as demonic as everything else. Zee Tee is one of them, but he is stuck in Flower-Man mode, and he needs the gems to turn into one of his own kind, even if it means killing his own kind to do it. And you helped him. You Bastard!!
Think about what the good ending means. Maybe Zeetee turned into something weird because of all the weirdness outside?
Maybe the rocks ARE the demons, appearing along with the rest of the evilness, disguised as harmless rocks until it becomes evil enough for them to emerge?
The game mentioned that the princess had been kidnapped and you had to save her. Well, we get to see the princess. Now imagine what the kidnapper must be like.
Imagine if the ghulibas were aware of what was happening to them. They'd experience gradually transforming from happy, frolicking creatures to lifeless frozen blobs to crazed blood-thirsty monstrosities.
Alternatively, if you interpret the multiple layers as causally linked alternate realities that exist all at once, it would just look like Zee Tee disappeared whenever he everted. That is, until he started fighting the monsters in that reality. Just when the X-1 ghulibas think their enemy is gone and they can return to their cheerful lives, they start dropping dead one at a time from spontaneous head trauma.
In the endings, we are to assume that the princess is a Humanoid Abomination. But think about this: in the secret ending, the world goes into the 4th eversion stage, and the princess completely freezes in place. So what does this mean? The princess isn't a Humanoid Abomination, she's being affected by the eversion. Whether this is better or worse than her being a Humanoid Abomination is up to you.