It's funny but back before this article came out, I saw somebody on youtube theorizing the same kind of thing. (Unfortunately I've no idea what video it was or who the poster was. I tried finding it and had no luck) But anyway the youtuber was thinking that Discovery is a Section 31 ship, if you'll recall that was the secret unacknowledged black ops group within Starfleet that featured most in DS9 and a little bit in Enterprise. And he thinks the spore drive, which they say accesses some sub layer of space to instantly travel, will cause some disruption in reality. He's thinking that as they keep using it reality will shift or be altered somehow leading to the Klingons changing to look like we expect them to, for the technology to change and look less advanced like TOS, for Spock to forget he ever had human "sister", etc. It's a good theory and would fix all the mistakes. And once they realize the spore drive is altering reality they will stop using it. And since they are the only ship with that drive, and part of a secret organization, that will explain why nobody else in the future knows about it. Then I see this article and have to wonder if the producers or writers saw the youtube theory and just going to use it now.