Well you and I have different understandings of cluttered. Scrolling down, and down, and down again, and down some more is a much bigger pain that opening a story in a new tab, reading it, and tabbing over. It also has the advantage of providing the author with the ability to earn rewards on the separate post, which has greater visibility than a nested comment. If the story is good, I'd want these comments to drive readers to the story itself so the author can be rewarded for content on top of the general interest it garners.
Different strokes for different folks, I guess. In the end, as long as people are writing, it's not relevant. At the end of the day it's @iamjustincscott's brain child. :D
I agree that scrolling is a pain, that's why I minimize a comment after I've read it. You can do that using the minus sign next to the comment.
Have you checked out the example I gave of how it works on Reddit? It's a wall of text and endless scrolling, but if you minimize what you've read, you can read it through in no time.
Of course, to each his own. If you still prefer linking to your post than you should do that. :)