I don't think that's quite true though. The game is saying that someone who plays by the rules (of physics) is not, by himself and in his underwear, the equal of someone who eats physics for breakfast.
Being two-faced about physics is intellectually dishonest. Either we apply the rules to everyone, or we don't. Imagine if you were playing a game a Monopoly and the rules say the Car gets $500 for passing go, but the Shoe only gets $100. There's no explicit benefit to playing the shoe to counteract it's handicap. While we're at it, lets say the Car can roll doubles all day and never go to jail. Furthermore the Car has the option to just move to whatever square it wants regardless of the dice rolls.
This is basically the problem that exists when we say that the Fighter has to play by the rules and the Wizard doesn't. The rules are arbitrary, they only exist because someone wants them to. So to take arbitrary rules and claim that they must be followed because they're "the rules" is very short-sighted and just plain two-faced.
This is about like admitting that a long infantryman is not the equal of an apache gunship or main battle tank. I fail to be amazed.
The apache gunship and the long infantryman play by the same rules though, the apache is more like a 20th level infantyman than a creature that plays by it's own rules.. The Wizard and the Fighter do not, and that is inherently the problem.
To make that infantryman the equal of a gunship or tank requires giving him superhuman powers. If your genre conventions forbid that, then you must look outside the infantryman and let him go to the quartermaster to pickup a stinger or TOW missile.
The Wizard already has super-human powers. The idea that the Fighter can't have them because he didn't read a magic book is just poor reasoning.
In D&D terms the fighter needs magic items, or a flying mount, or a team of guys with a catapult. You can do this.
Sure, but that still doesn't solve the original problem, it only covers it up with new layers that look pretty. The Wizard can still decimate castles, form their own planes, and kill with a word.
A flying mount is not flying. A team of guys with a catapult is not the ability to cast fireballs. I mean think about the logistics required to move, aim, maintain and operate a catapult. When you need a team of 10 horses just to move it and a quarry for ammunition, the guy who can guy "Shooba-dooba!" and wiggle his fingers still outstrips them in power.
What you cannot do is make a guy with a big knife the equal of a man who commands the elements and the forces of life and death. Or at least, not without turning him into Goku. And you also cannot insist that I play Dragonball RPG when I wanted to play D&D.
Then perhaps the problem is that the guy who commands the power of life and death and the forces of the elements shouldn't. I can however insist that there is no logical reason to say Fighter Dude needs to be bound to the laws of physics when Wizard Guy is not.
The laws of physics are either absolute, or they are not.
Do we want wizards who can do the impossible? Yes.
Do we want mighty warriors? Yes.
Do we want some semblence of parity between them? Yes.
Can we do that without giving the warrior supernatural abilities? No.
Can we do that by making the supernatural abilities external to the warrior? Yes.
To #3: yes we can, by nerfing casters.
To #4: no we can't. We can give them similar abilities in a few situations, but the comparable power levels will never match up.
Each of these can and should be a module. As for which one forms the 'base' module? Clearly a gladiatorial deathmatch is the only fair way to determine a winner.
If only politics were this simple.
4E was the first edition that gave all PCs the survivability and the tools (like At Will powers for spell casters) to possibly even be considered heroes who could hold off waves of attacking kobolds. Anymore, the word hero is banded about right and left. But when AD&D first came out, it was a word reserved for 4th level Fighters and NPCs out of Deities and Demigods. When AD&D first came out, PCs were Acolytes and Apprentices, not heroes. They were cautious because they were vulnerable, they weren't cocky because they were so tough.
By the RAW, yes, 4e significantly buffed players and debuffed NPCs.
In my game I buffed NPCs and almost killed my party in every encounter. ALMOST. 4e May have made PCs significantly more powerful, but it is fairly easy to tune up the NPCs to make them a credible threat. PCs are only ever overpowered if you let them be.