How is CR4 responses organized?

New comments are not always appended to the end

Yes they are when the "Flat" option is chosen.

I agree that it would be better for the email notifications to take you right to the new comment. That's how Amazon does it. Moreover, they include the new comment within the notification. This enlarges the email message from about 4KB to about 20KB.

Building upon guest's statement, at the top of every thread, you should see three gray boxes. Look for the statement "Comments: Nested" at the far right. If you click on this, you can change the format in which posts appear.

The default "nested" shows indented posts which are direct responses to comments previously made.

"Flat" allows you to see all the comments listed in simple chronological order, making no distinction between comments which answer the original post and those which are directed to a comment. To understand the context, take a look at the numbering of each comment. if you see a single number, the comment is directed to the original post. if you see something like #7 in reply to #6, then you'll know it is respond to a previous comment - and you can click the "In reply to #" to see the comment.

You can toggle individual threads between these options or change the default to "flat" if you prefer.