It doesn't give a date on when project R was started in the mission "Target Acquired", it could have been being developed before knights came, I mean making massive, gun puppies made of nearly indestructible metal, that can fire off massive lasers that kill within a second of contact, 6 rockets that deal amazing amounts of damage that can pierce a nearly indestructible metal/alloy, fire off a barrage a 20 or so energy balls after firing said rockets, fire off a barrage of rockets, that deal a little less than the first rockets, stop for a second to change position, and then repeat without taking more than a second pause, wouldn't exactly take a day or two. And, @Vohtarak, Basil is keeping within clockwork terminals which enemies don't spawn in, and he could (if my theory that Strangers actually have hidden strength) could get through the clockworks, or take a secret passage that only he knows of.

And what I was saying is that the Strangers were in conflict before knights came. When walking to Haven after crossing the chasm, their are ruins of building, and they aren't fresh, the knights haven't been on Cradle long enough that destroyed building wouldn't be covered in moss. Which shows that conflict arose before knights appeared.