The reference style is my mnemonic to the order as well as where the parentheses are for non-reference links: since the reference definition uses []: then the reference uses [] too, and since the reference comes naturally after the text, then a non-ref link has the URL in not-[], hence (), and after the text too.

IOW I just think about "inlining" the reference, which would have otherwise used [] everywhere. Feels much more regular that way around.