Southern Comfort was released in the United States in 1981, although it is set in 1973. US forces withdrew from Vietnam in January 1973, after the signing of the Paris Peace Accords, which officially brought the conflict to an end. As such, the film is set immediately after this withdrawal, with the moral of the US army at its lowest ebb. Additionally, when the film was made in 1980/1981, the US was still in the midst of a collective post-war angst, finding it difficult to accept the crushing defeat which it had experienced at the hands of the, apparently, inferior Vietnamese. As such, both the date of the film's setting (the immediate disappointment of defeat) and the date of its release (the long-term ramifications of defeat) are relatable to the conflict.
The argument that the film is a metaphorical depiction of Vietnam primarily concerns the depiction of poorly trained, ill equipped, overtly aggressive US Soldiers being in a territory where they don't belong and being butchered by a more skilled, but technologically inferior enemy who knows the terrain and is able to use it to their advantage. The film depicts an alien swamp (a substitute for the jungles of Vietnam), and a group of soldiers fighting an enemy they cannot see and a culture they cannot understand. The soldiers are in fundamentally 'Other' territory, out of their depth and unable to deal with the simple tools of the Cajuns (such as the bear traps and the impaler). All of this has obvious parallels to the Vietnam conflict, where the US army were seen as being in a similar situation; a group of overtly aggressive soldiers fighting an invisible enemy on a battleground they could't get to grips with, and in the midst of a culture they could not (or would not) understand.
Continuing the metaphor, the soldiers are depicted as not properly trained, not psychologically ready for combat, and lacking in discipline and motivation. They are without proper leadership (after Poole is killed), and they completely disregard the rituals and culture of the native people who they encounter, feeling they have the right to ride roughshod over these people for no reason other than the fact that they are US soldiers. Stucky's fatal decision to fire the blanks at the Cajuns is itself a metaphor for the actions of many soldiers in Vietnam, unconcerned with the ramifications of their actions, ignorant of the impact their actions may have on the local people, and ultimately shocked that their actions prompt resistance.
The film also incorporates the sense of paranoia which was a major factor during Vietnam. The soldiers are being hunted and summarily executed by an unseen enemy, never 100% sure who that enemy is, and when and how they will strike next. This uncertainty creates fear, which in turn creates paranoia. As already explained, ignorance is also paramount amongst the men. Ignorance and paranoia is a deadly combination, as not only do the soldiers find themselves unable to understand the Cajuns, they actually misunderstand them. This situation is most obvious in Harden's interpretation of the innocent goings on in the village at the end of the film. He sees the men stringing up hangmen ropes, sharpening knives etc, and he automatically assumes something terrible is going to happen, that the whole village is in on the hunt, and everyone is part of a conspiracy to kill the soldiers. This type of unfounded paranoia, born of fear and ignorance, is often blamed for such real life incidents as the My Lai massacre.
Finally, to attribute a thematic point to the Vietnam metaphor, the Cajuns in the film, although they are ostensibly the antagonists, are not the traditional 'bad guys' of classic filmic narrative. As the Trapper says towards the end of the film, they are simply protecting their home (although it could be argued that they do take that sense of protection to an extreme) from an intrusive, unwanted and inconsiderate invader. As such, the intention of the film seems to be for the audience to have at least some empathy with the people whose territory is being invaded, an interpretation which could be extended into the political arena and suggests the film is in fact sympathetic towards the native Vietnamese people.