The usual procedure was to bring the ship into the wind, then drop the anchor while making sternway. Unless there was a very tricky confined harbor, they wouldn't drop the anchor while still moving forward. I haven't actually tried backing sail that much yet. Even if that method works well, I would still say that the issue is the large disparity in deceleration time of luffing up under full sail vs drifting under bare poles.
Those are fantastic articles and definitely read them. I think your simulation already jives nicely with the information they contain.