Yes, version 2.0 of the game no longer had that issue. I think he was afraid he would lose credibility in the gaming community. That was about the time when other games were starting up and he decided to go straight.
His model is still more accurate than others, within individual seasons, but as we see here it does not translate well to all-star rosters across multiple eras.
Still, the game is reasonably transparent, and once you accept the idea that a 4.50 ERA is a good season in a live draft or $200 million league, not so bad.
HAL could be better, and all the other complaints, but other games have their issues as well.