....Also, it appears to me that all the threads are linear, meaning that if I want to respond to the second post in a fifteen post thread, my response comes at the end (sixteenth post). Am I missing something?...
The best way to do this; respond to a specific post in a thread of 15 posts (or 200 for that matter) is to go to the specific post you want to respond to and hit "quote" in the upper right of that specific post, which will quote it at the top of your message (as you can see above in this post). This will allow everyone to see what you are exactly referring to if you are being specific to one post within a thread of many.
As you can see from me "quoting" your post, you can edit the quote itself so if it is a longer post and you just want to respond to a specific part of it, you can take out as much or as little of the "quote" as you like.
Hope I didn't muck up the waters any further for you with this explanation...