They did this to protect the image of the GTO. The Firebird was 150-200 lbs. lighter than the Goat, and had better exhaust manifolds, but both engines were identical. In every road test I have where a Firebird and the GTO were present, the Firebird was always quicker by at least 2/10 of a second. Of course, the road testers had always removed the throttle stop.
But as far as Pontiac image was concerned, the GTO was THE flagship car. Pontiac rated the 350 hp GTO engine as 330 hp in the Firebird, and the 370 hp GTO RAIV was 345 hp in the Firebird.
The inside story was that they were trying to keep the 10 lbs. per hp (an unwritten GM law) in effect to keep the insurance companies happy. The 3450 lb RAIV Firebird at 345 hp verses the 3700 lb. RAIV GTO. Problem was, there WAS no corporate policy, it was really just an insurance gesture. For proof that GM didn't really have a "rule", I give you the 396/375hp Camaro weighing in at around 3500 lbs.
When Pontiac engineers ran the new 1967 Firebird 400 by GM top brass, management felt the Firebird broke their little rule of 10 lbs. per hp. But the engineers were all finished with the 1967 Firebird, and they weren't going to change anything last minute. Fact was, it was a lighter, smaller, better handling version of the GTO, and everyone knew it. In order to appease top brass, the engineers cobbled up a make shift throttle stop, and that stayed in place until 1969.