Thanks for the thoughtful reply!

Actually, most of my defensiveness comes from an observation that whenever theism came up in a main article, easily defeatable young earth creationists were prominently featured.

Ah, that makes sense. I have a better idea where you were coming from now.

Is it a custom here to make such adjustments to an existing essay, or would people think that I did the changes to make their criticisms look unjustified?

Yeah, I think it's fairly common to make minor edits to a post. If you make a major change (adding or removing whole sections), then it might be helpful to include a note somewhere (e.g. at the bottom) saying that you've made such an edit just so people don't get confused.