The Goal of the Flower Game is to Win. The Winnower wants to Prove it's Logic(Sword Logic), so does the Gardener, which wants to Prove all Life Should Exist.
This is the back and forth conflict in which the Flower Game was pushed into our Universe.
If the Winnower Wins.....the Game Ends.
If the Gardener Wins......the Game Ends.
When the Game Ends, so Does the Universe. So both the Representatives of the Darkness/Winnower and the Light/Gardener, which would be the Witness and the Traveler, both Need to be Destroyed by Us, to throw the Game into Stale Mate.
Both Logics live within us. Proof. In the EDZ, there is a Scannable of a Shard of the Traveler where both Logics, Light and Dark are in Harmony with each other.
"You have no Pieces left to Place" - the Witness
That Qote is very strong and meaningful as it's like a Game of Chess.....the Witness is declaring Checkmate on the Traveler. Because the Traveler Lost it's Queen, but, it still has a Pawn near the other side, it's just how the Traveler plays it's next move, will determine the outcome.
So to your Statement, the only Reason the Winnower would be helping us.....would be so it can Win.
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This isn't entirely accurate. In the lore, the game between the Gardner and the Winnower ended once before. They wiped the game board, established new rules and started over, which is the game our guardian is currently playing.