I agree with the overall statement that the Bulletin should not have published this article as it is and definitely should have not tweeted what it did. Yes, they owe you an apology but I also don't understand some of the claims in this letter and think that these (maybe?) exaggerated claims undermine your good arguments and the rightful question for an apology.

First, concerning this paragraph:

I also have concerns about the nature of Torres’ background work for article — they seemingly sent every person that was acknowledged for the book a misleading email, telling them that we lied in the acknowledgements, and making some reviewers quite uncomfortable.

Where does this information come from? The twitter thread you link to does not claim that Torres' made the author of the thread uncomfortable, only that he choose to ignore the email. Furthermore, the mail Torres wrote to him does not claim that you lied in the acknowledgments. 

Second, the Bulletin did add an annotation to the article, correcting the claim from Torres that several researchers were not consulted. Yes, the article still suggests heavily that they weren't and even with this annotation you get the impression that MacAskill was at least negligent in his research, but accusing the Bulletin of just lying regarding this, is also not true.