Well, from events at the end of "The message back" it looks certain that they are from another planet in our present time whose residents are about to suffer the effects of a super-nova from a near-by star. (Though there's no explanation of how they were able to receive a response to a message they sent only days ago.)
So they are aliens at least in the sense that foreign nationals are aliens. I suppose they could be aliens in the ET sense since they *ARE* from another planet, but their compatible DNA will still need some explaining.
In Stargate Universe it was explained as the goa-uld (sp?) taking humans from our planet and moving them to other planets. Different planet life could make them similar but still different by as little as 1%... But no idea how they'll explain it here.