As far as I remember, The Tollan phasing device was introduced before the details of how the iris works were explained toroughly.
Indeed, the first time the iris is introduced, they don't really say much about it. This extract is taken from the Gateworld transcript of the pilot episode "Children of the Gods":
SAMUELS: (into radio) Close the iris! Close the iris!
O'Neill starts down the ramp, but he stops and turns to see the metal "iris" suddenly slide across the wormhole, contracting much like the iris of a human eye. O'Neill, Carter, and Daniel stop and stare as the iris closes, completely sealing the Stargate.
INTERCOM: Iris locked.
The security door slides up, and O'Neill turns to General Hammond, who has entered and is standing at the base of the ramp. We hear, but cannot see, the wormhole shutting off.
INTERCOM: Wormhole disengaged.
O'NEILL: What the hell is that, sir?
HAMMOND: That's our insurance against any more surprises. (as the iris slides back) It's pure titanium - hopefully impenetrable.
Hammond's attention turns back to the ramp, ...
And that's all we hear about it in that episode.
At the time, when someone was attempting to go through the gate with the iris closed, there was a big thud similar to what you would expect if you launched someone against a solid wall. I think the iris was even see moving in some instances. All this doesn't seem very consistent with the "matter doesn't" even reintegrate" iris theory.
So at first the iris was just this impenetrable barrier, and since the Tollan phasing device existed to penetrate otherwise solid objects, it was logical that it could penetrate the iris as well.
The iris was later destroyed and replaced by a trinium-strengthened one in episode "A Matter of Time" but I don't think then explained much more even then (no transcript, and I can't be bothered firing up the DVD right now). Maybe they said a bit more in episode Serpent's Song when Sokar was firing a particle accelerator at the iris.
In any case, I don't know when the 3µ explanation was given, but it was certainly after the Tollans were first encountered in season 1. (I was so wrong about this: it was given in episode 102)
So in my opinion it's one of these small inconsistencies that they didn't really bother to explain in canon.