Opus developed amnesia during the incident and found his way back to the Bloom Boardinghouse, and told everyone what had happened once his memory returned.
(In those days his name was given as "Saigon John" and his war injury is described as taking a shot (presumably friendly fire) while smoking a bong (improvised from his M16) with a North Vietnamese soldier, making his tunnel rat story presumably a retcon.)
His more familiar name is most likely a reference to Trapper John McIntyre from M*A*S*H. While a major character in the first half of Bloom County's nine-year run, his role was reduced to only occasional cameos for the remainder of that strip and its immediate spin-off, Outland.
In the commentary in one of the Bloom County collections, Breathed observed that he dropped Cutter John from the strip because it was too artistically challenging and "frustrating" to draw someone sitting down in every panel of the comic.
His sole appearance in Breathed's last strip, Opus, comes in a one-panel cameo, alongside Bill the Cat, Michael Binkley, Milo Bloom, and Oliver Wendell Jones, when Steve Dallas "flashes back" and sees them shortly before going to see Opus in the Animal Shelter in the strip's final storyline.