This post is definitely not site policy, and at least I as the site admin disagree with any kind of "should" here.

People are already too hesitant to downvote content on the site. Explaining your downvote is good, but do not feel any obligation to do so. The voting system is anonymous for a reason. Use it for expressing what your values are, approximately whatever they may be, even if you cannot put them into words.

I agree.

I often write an explanation of why new members' posts have been downvoted below zero, when the people that downvoted them didn't bother. Downvoting below zero with no explanation seems really un-welcoming. I realize it's a walled garden, but I feel like telling newcomers what they need to do to be welcomed is only the decent thing to do.

I am against this from both sides. Some things just aren't worth more than my downvote. And when I get downvoted, as a couple of my recent comments have been (strongly, even, as well as some strong upvotes), it's generally easy to see why, and I'm not interested in extending the conversation. I said a thing, some people didn't like it, we disagree, we're not going to agree^[1], move on, because the conversation would be nothing more than everyone repeating things already said. If anywhere is the place to not have such conversations, LessWrong is it.

I am strong down voting in this case as when I put a noticeable amount of effort responding to your prior post "are there 2 types of alignment?", you gave an unsubstantiative followup to my answer to your question, and no followup to the 5 other people who commented in response to your post.  

When I attempted to communicate with you clearly and helpfully in response to one of your low effort questions, I saw little value. Why should others listen to you when you tell them to do what I did?

I've noticed at least once that I've downvoted a newcomer's post for no other reason than it is so vague or incomprehensible that I'm not even sure what it is about. I'm not sure how to go about writing comments that are useful or helpful and go beyond "This is all really abstract and I'm not sure what you're trying to express" or "This is so confusing I don't even know what the topic was meant to be". I don't know if that helps anybody, because it's not even giving them a flaw that they can meditate on.

What's a better way of addressing that confusion?

The only alternative I can think of is guessing what the author meant, even if it's wrong, and hoping that you can Cunningham's Law^[1] them into correcting you in a way which is clear enough to understand. 

1. ^{^}

   The joke that the best way to get the right answer on the internet is by offering the wrong answer

It's crucial that some people get discouraged and leave for illegible reasons, without a need for hard enforcement, which has unwieldy externalities. For almost everyone who should stay, figuring out reasons for significant downvoting is probably not very difficult. Any discussion would then be about correctness or endorsement of those reasons, not about finding out what they are.