I agree with you there, to win the case there would have to be some economic reason for Slack to not want users to use this extension.
The reason they state is "Injecting javascript into Slack via Chrome extension can have an impact on the privacy and security of our customers and our product. Furthermore, this can create reliability issues when we ship product updates." If they can prove that is true then the case stands up but if BetterSlack doesn't impact security, privacy or reliability then the case would probably be dismissed.
If it alters the DOM, it impacts security, and in a very significant way, since DOM security is in a sense the most important security barrier between untrustworthy content and all the messages a user has access to on a Slack.
Sure, it "impacts" security. But as we are discussing above, it would need to be shown to "negatively" impact security. I don't think you could win on the basis of "it's not recommended to do that, but we can't see any examples of it actually causing security problems."
The reason they state is "Injecting javascript into Slack via Chrome extension can have an impact on the privacy and security of our customers and our product. Furthermore, this can create reliability issues when we ship product updates." If they can prove that is true then the case stands up but if BetterSlack doesn't impact security, privacy or reliability then the case would probably be dismissed.
There's some excellent analysis of this sort of case here https://ir.law.fsu.edu/cgi/viewcontent.cgi?article=1101&cont...