Analysis of that Eagles Super Bowl defense is interesting.
Calling that defense a 4-3 or a 2-5 is a matter of semantics.
The Patriots used two DL and five LB, so you can say 2-5.
They lined up with LB's over the tackles, so you could call them DE's.
However, an important point to consider is that the Patriots defense included multiple versatile LB's - Vrabel, Bruschi, Phifer, McGinest, Colvin, plus Johnson who was more one-dimensional. All of V-B-P-M-C had lots of experience at LB, dropping into coverage, stringing out the run, or rushing the passer. With six starting LB's, the team could easily run five in a single formation.
You'll also see how they were switching up. The descriptions show Green at NT one play, then Wilfork at NT the next.
Here's an example showing the ambiguity:
Patriots Defense: 4-3, Colvin down over TE, Green over LG, Wilfork NT, McGinest down over RT, Vrabel comes up over Owens in motion, Gay follows across the field, Bruschi and Phifer playing back, Samuel press coverage
Result of Play: McGinest stands up to chip Owens before Gay picks him up, then comes out to force McNabb to toss it over to Owens in the flat, Wilfork got pressure but Colvin and Green were stopped, Vrabel started to come in before the throw.
What you see in that formation is McGinest lining up 'down,' or in a DE stance, over the RT. Colvin is in a DE stance as well, but over the TE, where he might also play as a LB.
At the snap, McGinest stands up, rather than rushes, chipping the WR. He instantly becomes a 'LB' when he stands up at the snap, switching from a '4-3' formation to a '3-4' formation. Colvin rushes like a DE.
The whole point of this defense was confusion and athleticism.
The Philly offense that season was very pass-heavy and run-light. Their best RB was very much in the Marshall Faulk role - more likely to take a short pass a long distance, less likely to try to run straight up the middle.
Playing Jarvis Green at nose, with five LB's on the field, is a defense designed to flood the intermediate zones but very susceptible to a power rushing attack. Like the Saint Louis Super Bowl, Belichick is daring the opposing coach to run the ball at him while taking away his strength. Reid stuck with his strength. McNabb couldn't anticipate the pressure or the coverage, and had a poor game.
Now look at the '4-3' described in training camp. This is an entirely different defense. Warren-Wilfork-Sullivan-Seymour is a line-up of four DT-types. The Philly game was a line-up heavy in LB's, the strength of the team. This line-up is heavy in DT's, the current strength of the team. By replacing Green, Colvin, and McGinest with Warren, Wilfork, and Sullivan, you are going jumbo.
This 4-3 is more like something you would throw at Pittsburgh, attempting to choke the line of scrimmage. A team like that Philly team, or the Saint Louis Super Bowl team, would screen over it and slice it up.