Hey, I replayed the game, more or less going through it pretty easily.
there is still stuff I dont have/get:
the last item
then there is the one place bottom right where there are 4 pictures shown (3 are the 3 bosses and have a red light besides them. forht one has a green light and I am not sure if it's a boss and item or whatever. kind of expected to stumble upon that last thing when backtracking but no idea. looked literally everwhere systematically)
and obviously the new dimension :-)
but mostly the last item and the 4 pictures with lights next to them, suggesting to me that there should be a forth boss that I havent defeated yet and that something will happen there afterwards.
You're in a Jailkeeper's ship so... could it be the panels are displaying the prisoners and their status? Maybe a green light means the prisoner is still safely in custody, but a red one indicates they escaped? :o
I'm goofing around, but don't worry: you've already defeated the boss with the green light. (It was the big eye thingy! That panel is a bit of foreshadowing for the final boss, and one of the many hints for the shocking reveal!)
I'm guessing the item you're missing is a Trophy, either for a secret boss or the reward for collecting all the Strange Eggs. If it's one of the bosses, one of them is behind a closed door in the temple, and the other is buried under a tombstone. Hope this helps!