There is, indeed, a lot of logic and circumstantial evidence supporting that notion. I hadn't thought this element through but, upon reflection, am inclined to agree -- Iraq could well have been calling the shots on the WTC attacks.
Another observation inferentially supporting the idea: recall how much evidence was left behind in the automobiles, clearly implicating bin Laden? It smelled so much of a set-up that I was initially inclined to disbelieve it -- but couldn't figure which terrorist group would benefit from laying a false track. However, it would clearly be beneficial for a terrorist state, wouldn't it...?
I'm inclined to think that, in a sense, Iraq is taking advantage of al-Qaeda, just as al-Qaeda took advantage of Afghanistan. In each case, the side with the disadvantage thinks that it's getting what it wants, and maybe it is, but maybe it's just being used.
Iran and Iraq appear to be in this roughly as equals. (Iran has clearly been supplying the Palestinian terrorists, for instance. Iraq also been making payments to the families of the suicide bombers.)
The big question is: What is China's role, if any? This is entirely speculative, and there's certainly no evidence, but consider: Who would benefit from a protracted war between the Muslim world and the West? China. The Chinese could just sit back and watch while their two major enemies weakened one another. Is China goading Iraq, pretending to help it but actually just fueling the fire?