I really like being able to use footnotes, which unfortunately don't work well with Kindle-style flowing text.

I find it useful to explain some concept that most readers probably know, to bulletproof ("yes, I'm well aware there are one or two edge cases but they're really not relevant in general. Let's move on."), historical digressions that aren't important to the general point, and references. (Of course, if it's only references, those work fine as end notes.)

It also helps for comments with multiple links to have a footer with all of them.

I made no assumptions of your competency. What I said was obvious to me but, your comment indicated that you didn't understand why people use footnotes on HN. To effectively communicate ideas to the largest number of people it is necessary to follow conventions. Bucking convention reduces your possible audience size.

I think have higher standards for obviousness than you.

My comment did not indicate that I don't understand footnotes, not here nor in books, that was something you read in. In fact, my comment indicated facility with the subject. A person unfamiliar with footnotes wouldn't even know to call them footnotes, and a person unfamiliar with how they are used on HN would not say "(a) I disagree with how they are used and (b) because links are highlighted to stand out they are not a distraction". What I just wrote there is obvious to me, why not to you?

nobody knows at the beginning of a comment whether later in the comment conventions are going to be bucked, and I highly doubt in a 4 line comment whether inline links or footnoted links are going to make a difference to audience size, i mean seriously!

You call it the most interesting thing I've read all day, I call it boring bikeshedding, but I won't downvote it regardless.

Pedantic, off-topic comments also break conversational flow.