To me, this film if a mythical exploration of man's nature (a civilised killer, who is ordered to kill a man he might well become) which explores deep themes of mans warrior essence.
It was not intended to be historically representative of the Vietnam war, but a representation of man at war in general, which used the Vietnam war as a canvas upon which to paint it's own story.
I deeply admire the sound design by Walter Murch which arguably changed all action and war movies since.
The storyline of Phoenix and Rogue SOG is obviously complete hooey, although there were legendary shadowy figures gadding about back then, just read some of the SOG vets memoirs and hear them tell of RV-ing with CIA operators deep in the jungle, or prowling the backstreets of Saigon looking to murder a french VC assassin. Some crazy tales are buried in the memoirs, and almost nothing is ever spoken about regarding the Phoenix Program.
It's a great fun movie to watch, but doesn't tell the story of the Vietnam war at all, it's way too generic.