Why is the "In reply to" indicator suppressed sometimes?

the problem with this is: without threading and without an indicator, the replier may not contextualize his comment as in response to the above comment. after all, he hit the reply button, so it’s obvious to him. it’s obvious to the person responded to, because he gets an alert to his profile. but to all other parties reading the thread it is assumed that the post is in response to the topic. without heavy context clues by the poster (who isn’t thinking about leaving them, nor should they) their response may not look like a reply to the comment above it. that it is one might be contextuallized at the end, which requires of the reader a mental shifting of gears and perhaps a re-parsing.

tl;dr “is this guy replying to the topic or to the post immediately above? i will scrutinize it for context clues that may or may not be there. gee, homework is fun.”

i know it’s a design issue but it was in this thread.