Yeah, the whole DNA angle of the initial run wasn't clear. Originally I thought the Alpha's different appearance was due to it coming from a Goat-Queen, but then everything coming from the Alpha was largely "typical" and we saw a couple of Runners but that's easily worked away with them using livestock as hosts too. So...yeah...it's just unclear.
As Tilotny says though, the Aliens in the new arc have (as far as we know so far) nothing to do with the outbreak on the station.