It's answered in the novel Department of Temporal Investigations: Watching the Clock. Spoilerific click!
More recently Brannon Baga has started claiming that he was supposed to be a future version of Archer, but I'm pretty sure he's just attention whoring because that makes less than no sense. Click!
Had he not been killed off In a Mirror, Darkly, I think it would have been kinda awesome if Future Guy=Mirror Universe Archer.