So, I preface this by saying that I do feel like Slack could have better authentication mechanisms, decoupling the account from the networks. But I do think that some of this is by design as well.
I think it is worthwhile to think of each Slack organization as a completely independent and isolated network. This is one way that they can reasonably give some security to their corporate customers. I don't believe that there is any intention to ever lat you send a blind message to someone on another Slack organization, but maybe I am wrong there.
It would absolutely be nice however for me, as a user who is in multiple organizations, to be able to log in one time and have all of them be connected.