Very interesting comment.... but its very ambiguous and misleading.... before i tackle each of the replies.. i will give my TWO CENTS then read the other comments on here.
"As far as we know"
Is to me aimed at the Viewers... Fassbender would know for sure, and so he means as far as We the viewers and maybe David and Shaw did from Prometheus.
Here is a run-down of the possible outcomes.
1) Engineer.... a Engineer or Engineers could be possible, we see that in Prometheus only One Survived in Cryo-sleep the other 3 in that Ship Bite the Biscuit... (Chest Busted)... They have taken another ship and we cant rule out other ships having Engineers too.
However.... i would assume Shaw would no doubt check the Cryo-Pods out before hand, before putting David back together and if there was Engineers... i am sure that Shaw would either
a) choose another ship....
b) ask David if they can be killed...
c) ask David to wake them up and get her Questions answered.
2) Deacon.... could the Deacon had got on-board? The timescale of the movie showed and artwork that the Deacon had happened after David and Shaw had left.. so NOPE the Deacon is not on board.
3) Milburn.... or any survivors.. I would say Milburn is dead... maybe he is Gestating something laid by the Hammerpedes but how would they follow David and Shaw on that ATV or get on the Buggy? Same goes for any survivors.. there is NO-Way any other Humans or anything related to Milburn gets on board.
4) Cargo.... straight up we know the ship has Cargo, Ridley even said it would be carrying Hell with it.. in regards to the Black Goo.... so technically yes the Black Goo is something on-board.... but the "As far as we know" comment applies to the viewers and maybe Shaw... and as far as we know.. we do know it has a Cargo and Shaw does and i doubt she would want to choose a ship that has none.. or get David to unload the Cargo... The Cargo is also a insurance a Bargaining/Deterrent chip if the Engineers are not so friendly..
But as far as we know... we are assuming and maybe Shaw too that the Ship has Black Goo Urns... it could actually have something else. Maybe Eggs? who knows.. Make the whole how did David get Eggs Question more easy and then leave the Xeno Mystery in-tact.. Do we know the other ships all have the same Cargo? Or if anything has evolved in one of the bays?
But Nope.... i think the Ship has Black-Goo.
5) Hammerpedes.... well Worms.. they have taken another ship and we dont know if its from the same Temple in another Hanger or another Hanger in another Temple. Worms are tiny and they could easily get on the ATV, into Shaws Back Pack... and even if not... they are somewhat indigenous to LV-223 or at least have been on that World prior to the Prometheus.. and so there is a chance a Worm or other small native Organism could creep on-board.
If there is anything to Fassbenders Comment and AC wishes to somehow connect Prometheus 2 and LV-223 and Black Goo to the Xenomorph... the Worms could be used as a Plot Device.
When i look at LV-223 and the Space Jockey and Chest Busted Cryo-Engineers and how the Hammerpedes were under-used.. and looking at the Life-Cycle of Worms..
Right now and well from a long while back... HAMMERPEDES are certainly a potential possible link to the Xenomorph that would not contradict the timeline...
2093 Worms + Goo = Hammerpedes.
2000 years prior Outbreak... and who is to say the Goo 2000 years ago.. or 2000 years time + Worms = Hammerpedes again..
Its logical and what the Source somehow implied.