Nested comments do not exist in Q2A. Adding that feature is definitely a complex and long task.
The "Reply" button is tricky. It is displayed in each comment and that gives the impression that clicking on it, somehow, links the new comment to the one on which the button was clicked. However, this is not true. The reply button has a similar behavior to clicking on the "Comment" button of the parent post.
So comments are stored all at the same level and are displayed as a chronologically ordered list, one after the other, no matter how you add them.