Why does the 1998 Trigun anime end differently from the manga?

The arithmetic is the whole answer. Madhouse's Trigun, directed by Satoshi Nishimura with series composition by Yosuke Kuroda and music by Tsuneo Imahori, aired for 26 episodes on TV Tokyo from April to September 1998. At that moment the manga's original run had already been cut short by its magazine's closure, and Trigun Maximum had only resumed in October 1997. Nightow would keep writing it until March 2007, nearly nine years after the anime ended. The documented summary is plain: despite being an adaptation, the narrative differs in the second half because Nightow was still writing the manga at that time.

So the anime built its own road to a finish. Kuroda proposed that Vash not fire a bullet until the fifth episode, so that Meryl's realization lands as a reveal. From there the production gradually reduced the early comedic tone in favor of more dramatic storylines, and the introduction of Nicholas D. Wolfwood in episode nine shifted the series again, with Wolfwood written as both Vash's ally and his rival. A 26 episode broadcast series could not stop where the manga stopped. It needed a confrontation with Knives, and it wrote one.

Nightow's own verdict on the result is on the record, and it is not a complaint: after assisting Madhouse with the adaptation, he considered the work faithful to the manga and credited it with helping him properly serialize the story. The two endings are not a betrayal and an original. They are a finished broadcast invention from 1998, and a manga ending that did not exist until years later.