For the last time there are spoilers so if you don't want to know don't read.

While it's a good standalone story which I greatly enjoyed, especially Sandor Cohen's brief reappearance, I don't think it should be cannon for a couple of reasons.

1. The Daisy Fitzroy Revelation: where its shown that she was just play acting for Elizabeth to make her a women.

Bioshock has always been about warning of the dangers of radical ideology. It was shocking in Infinite how far over the edge Daisy went as a result of taking her revolution too far, but this development just took that all away. At one point Comstock and Daisy were just as evil, but at opposite ends of the spectrum. Now Daisy is basically a good guy taking all the steam out of that message.

2. Atlas acting crazy evil

Everyone who played the first Bioshock know he's secretly evil. But no one else is supposed to. The entire reason people joined "Atlas" in Rapture is because he was a charismatic leader who appeared to care about the lower classes and have their best interests at heart. Changing that to him being basically the head of a large gang in a makeshift prison ruins that character for me. It would have been better if he had acted like the good guy but with sinister undertones.