FWIW, I disagree: I think in (2) edit: the general case of [text](URL) (call it (2a)), the link URL should be rewritten the same way as (1). (I agree that the current behavior of rewriting the text and not the URL is completely broken.) I make the decision between writing (1) and (2a) based on whether I think it’s useful or distracting for the URL to be visible to the reader, not based on any intent about whether the link should point to the version of the code as of writing or as of reading. Of course, I’m aware of the permanent-link issue, so I make a permanent link myself whenever I want one. But more generally, if a Discourse administrator decides to enable the permanent link bot, presumably that’s because they think most of their users aren’t aware of the risk that branch-name-based links can rot, and I don’t think the use of the Markdown link syntax is much of a signal that a given user is aware of the problem but wants to opt out of that particular link being rewritten.
But I think we’re both just speculating here. As an advanced user, I don’t care much what the default is as long as I can override it as needed.