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The Tree of Life is a Kabbalah reference. It is the Sephiroth tree, which *is* the human body:
So actually, the Tree of Life is meant to flesh out the riddles for those who know stuff about the Sephiroth (and also a Black Cat tie-in in a way). It isn't a separate puzzle.
It's also a Wizardry 4 reference, since the final dungeon in Wiz4 was modeled after the Sephiroth Tree aka Tree of Life.
So, once you've got the puzzles figured out and got the nyin, just go through the door. For an additional easter egg ending, try using the Neanderthal Sense repeatedly in the next area.
Also I hope you got the lava room ending already, since it kind of complements the ending you're about to get.