It has been suggested in another thread that the underlying theme of fallout 4 is freedom, which I believe to be true. This ties in with the way that the devs have explained various aspects of gameplay, with the entire point being to allow the player as much freedom as possible. If this is true, then why would they force us to have to use such an exacting system just to unlock anything other than the first rank in each perk? The simple answer is that they wouldn't. First of all, this would create a bias for the 4 perks that have only a single rank. Secondly, it would seriously restrict, and even dictate, our play style. Say I wanted to play as a stealthy character who will eventually use a sniper rifle. I sneak around taking pot shots with my hunting rifle that I found early on, but instead of modifying it just yet, I choose to gather resources instead. Why should I be prevented from unlocking subsequent ranks in Gun Nut as I progress just because I have not yet modified my weapon? Again, the answer is fairly obvious.
And so, it would seem that I have not over complicated anything. All I have done is applied common sense, as well as the universal principle known as Occam's razor. When a journalist who works for an official magazine says something that is completely different from information already confirmed by those who are actually making the game, logic suggests that they have misunderstood something along the way.