I can't decide if having an ancient, dilapidated ship spawning people to do a job that no longer even exists is right for 40K.
That sounds very 40k to me, actually. But doesn't work if we're supposed to seek out the ship as part of the first adventure.
Perhaps the reverse then. The ship is supposed to produce it's own crew and any other beings needed but it has been getting less reliable over time until finally it just vanishes. Now a Dynasty is left with the last batch of crew produced waiting in stasis to be awakened. Assuming that these false men will have some connection with the ship they are thawed out and sent to meet their maker.