In the ending of Puss in Boots: The Last Wish, Puss accepts that he has one life left, and Wolf, who is Death, spares him but says they will meet again. The deeper meaning is that fear of dying turns into appreciation of living, and the wish becomes unnecessary the moment Puss stops running. Puss decides not to use the wish, and that choice is the point of the whole story.
Why does Death let him go? Courage is the whole point of the scene. Puss spends most of the film fleeing, from the moment he realizes Wolf is Death and runs in terror to his retreat into a cat lady's home at the start. The moment he stands still and names the value of his last life is, in my reading, the first time he is not a legend performing bravery but a cat actually being brave. Death respects that, and the promise to return keeps the stakes honest, because Death is not defeated, only postponed.
The supporting endings echo the same idea. At the star's location, Jack Horner grabs the wish and the star's power consumes him, so a man who wanted all the world's magic gets the opposite of what he hoped for. Goldilocks gives up the map and stays with the bears as her family, so she also trades a wish for something she already had. Puss, Kitty and Perrito become a family and sail off on new adventures, and the film leaves the door open to more stories for Puss. The cleanest comparison, and again my opinion, is between the opening party, where Puss treated his lives as a currency to spend, and the closing sail, where he treats them as time to share.
The look of the film backs up that arc. Production designer Nate Wragg proposed making the film resemble a fairy tale painting, according to director Joel Crawford, and TheWrap's behind the scenes coverage describes Wolf as designed with a diamond shaped silhouette that the team could shift into a stark black, white and red palette for dramatic moments. That is why Death reads as a different kind of threat from Jack Horner, who is a spoiled crime boss. The opening rooftop chase, which Syfy Wire notes uses more hand drawn techniques, moves deliberately less smoothly than earlier Shrek universe films, so the style itself already signals that this story plays by different rules.
Against the rest of the series, the ending is also a break in structure. Shrek, Shrek 2, Shrek the Third and Shrek Forever After are the four main films, built around Shrek himself. The Last Wish is the sixth release and, in chronological order, also the sixth entry, following Shrek Forever After. It is the second Puss in Boots spinoff after Puss in Boots (2011), which comes first in the chronological order, and it gives Puss a story about mortality rather than a rescue or a heist. The film's closing sail is a farewell to the character as a solitary legend, and it fits a franchise that now looks ahead to Shrek 5, set for June 30, 2027.