We used to have a saying in my Time Code for Audio class at Berklee, and I'm sure most engineers have heard it; "The great thing about standards is there are so many of them!"
Manufacturer's specs are just that - what the manufacturer uses to setup a guitar coming out of a factory. and they do an OK job, when you remember what they are after. They are NOT trying to put out the best playing guitar you have ever held. What they are after is a guitar that plays pretty well, and will never, EVER, buzz while it is on the wall in the store. Why? Because they have been told over and over again by all of their dealers that if a customer picks up a guitar that buzzes, they will put it down and never pick it up again. Ever.
And you know what? If you are a Bluegrass strummer who is banging out chords and bass runs all day, that setup might work for you. If you want a guitar with a bit more subtlety to it (and that isn't a knock on Bluegrass), you are probably going to want a bit more carefully adjusted setup. And THAT is a highly personal thing. Some players (well, lets be honest, most of them) want their action as low as possible without buzzing. This depends on so many things, though, that numbers and specs are pretty hard to come up with accurately. They can be a starting point, but for a really good setup that is usually all they are.
Lets take two of my customers. Both great players; one of them is a world class acoustic fingerstyle innovator. He's been making records for more than 40 years now, and spends about 200 nights a year on the road. He is one of the best players in the world (no joke, he really is), and he pushes his guitar really hard (though not as hard as he used to). The other is largely an electric session guy, and does a similar number of gigs every year, though more of them are local. He also puts out instrumental jazz records, and does a fair bit of touring to support them.
The fingerstyle guy likes his action to fight back a little. His necks will usually have a bit more relief in them because he drives the strings so hard, and his action is a bit higher than others would prefer. I find his guitars pretty tough to play, but they are his thing. He's also pretty comfortable with things not being exactly where he might prefer (which is good, with as many climate changes as his guitars go through), so if things are acting up a bit he can bring the action up and be OK.
The session guy has had some health problems that keep his hands a little weaker than he would like. Because of this, he needs his guitars pretty easy to play, but he also needs to have enough room that he can get some real dynamic range (which you loose as your action goes down). So, his necks are pretty straight, and his action is pretty low. This leads to a bit of a problem for him, though, which is that his frets are critical. He ends up having to get his frets dressed (very lightly, mind you) quite frequently, because any small spot of wear will cause his guitars to buzz. (we've been moving him to stainless steel frets because of this, though he is always a bit skiddish about new things).
So who is right? Both of them. But they are not aiming for the same target. Fender is aiming for something that is tolerable by most people. Dan is looking for a starting point at a more complete setup.
Finally, if you really do want the "as low as possible without buzzing," setup, don't expect to get your guitar perfect yourself. It takes a lot of practice, and a lot of expertise.
Gabriel