Serious question: Why wouldn't they? It's not a throwaway scene either. It is the first interaction Gordon had with Bruce Wayne. Even if they don't remember the actual scene in question, when Batman says a hero can also be "a man who puts a jacket on a young boy to comfort him" I don't think anyone who is of at least average intellect and who is actually paying attention to the film and characters will not understand what he is saying.
Narrative objective: Batman is hinting to Gordon who he really is, while paying him a compliment for something he did for him when he was a kid.
- If an audience member has not watched Batman Begins, but is paying attention to the story told in The Dark Knight Rises, he/she will still understand what is going on, especially since Gordon himself says "Bruce?!" right after.
- If someone watched Batman Begins but does not recall how that scene played out exactly, he/she will probably still remember the general reference.
If on other hand, someone is still completely oblivious at this point, and really needs a direct visual flashback to go "Ah! So Gordon at some point in the past put a coat on Bruce Wayne when he was a boy! Oh!!!" then the entire scene loses further meaning because it is not about the scene itself happening, but why it happened and how it happened. The flashback does not capture any of that.