Interesting point about the problem of HN's depth-first comment structure. It feels like perhaps HN should collapse sub-comments by default to encourage more breadth. Perhaps collapse by default at the 2nd level.
Your approach to solving that is an interesting UX idea but even with the basic understanding the comments are sorted by their levels, it wasn't very obvious how to navigate the app. I kinda expected to be able to easily scroll across all level 1 comments (whether scrolling vertically or horizontally).
I was also surprised that the first comment was already pre-selected, and that level 2 comments were only for the selected comment. You could require new users to click on a comment first before expanding to show the level 2 comments, gives them an opportunity to learn the relationship between the two.
I'll keep brainstorming with the UX for the next version. I appreciate your perspective on how all the data disclosed on first load might be disorienting with unclear relationships. I'll play with either some sort of animation cue, colored or bordered visual indicators, or a default null selection as you've suggested.
