The problem here is the assumptions that a) there is a player available to fill your position of need via free agency (high value skill players aren't on the open market often) b) you can afford the player on the open market and c) the player signs with you over other teams (trades are a whole different can of worms, see the Texans).
With the draft you have a known amount of targets per position prior to the draft (QB X, QB, Y, QB Z). If one of those prospects is sitting there and especially with the QB position you make the pick. You might be able to argue between a WR or DE or LT and BPA but with regard to a QB you make the pick regardless of BPA if you're the GM.
Hindsight is 20/20 and there is a host of teams who whiffed on future HOF players due to BPA so all you can do is complete the roster the best way given the constraints at the time and that might be Free Agency, Trade, BPA or Draft for Need, you simply can't know since there are classic examples of all of those methods working and failing for a franchise,