He was mistaken. The Ames strain was actually a RARE strain used mainly by USAMRIID.
It was the BIG error by Ivins that eventually led to him being identified as the anthrax killer. His other incriminating acts were all the result of things he had to do because he made that first mistake.
He also believed incorrectly that the "single colony pick" method he used when preparing samples prevented the creating of mutations. It didn't. It almost guaranteed that there would be LOTS of mutations. That was the second error he made that helped the FBI make their case against him.
See my page about this HERE.
Smart people sometimes make very STUPID mistakes.
1. It's not so clear to me, even in the enlarged picture, that the T's and A's you specify are the only highlighted letters. (For instance the second A in 'Allah' looks like it has had some additional work. Some of the the O's, E's, and H's look funny too.) Maybe my eyesight is not so good. Maybe Ivins purposefully made it hard to detect. Maybe one has to compare all the anthrax letters to see it. It seems to me that you should clarify this in your book.
2. Why wouldn't a scientist like Ivins pick something more esoteric than Godel, Escher, Bach? He's probably working with DNA all the time. Why does he need GEB and a 1992 article on "DNA linguistics" to figure out a DNA-based code?
3. You make a point concerning the GEB idea of the framing of the code. But if Ivins wanted to step in later as the hero, he wouldn't have needed to point out that there was a code before this point. So he must have had a desire on some level for the code to be discovered earlier. Based upon your description of the code, it is not unlikely that a random person with a little familiarity with DNA could have eventually discovered the code. This would probably have narrowed the suspect list greatly, undermining the steps Ivins took to not be identified. Perhaps this makes some sort of weird sense if Ivins did not expect anyone to die. But surely he could have expected to be in a lot of trouble anyway.
4. If Ivins identified himself as the sender of the letters, he would also be identifying his obsession with his coworker and his obsessive hatred of New York. These probably wouldn't be compatible with Great American Hero status.
5. The three-word sentences thing might just be used to stress the number three. But maybe there’s another code as well. Sometimes a single strand of DNA can contain two overlapping codes.