There is very little in the v-notch of the engine under the intake manifold. Take a vacuum hose stick it in there and suck everything out. If you had any damage to say a knock sensor you would have known by now. I had a similar thing happened to me but not when of new.
Taking the intake off is not really taking the engine apart nothing to worry about doing so! For peace of mind I would do it and you can probably do it yourself if you are at all mechanical its just some nuts/bolts and a few wiring connectors and a fuel feed line very simple. Probably take all of two hours to complete start to finish!
They’ll probably say there was no nest when they handed the car over. You got a great price on this car and maybe have them clean it out and work a deal on that Ford premium extended warranty you were contemplating.