Many times, I see a flag (generally a custom one), and wish to reply to it. A common type is the "Convert to CW" flag that rears its head at times (it is helpful, since it leads to me closing the post, but the premise is incorrect). Such qs are usually closed as NC, so I mark the flag as helpful--but I have no way of letting the user know that their premise behind the flag is wrong aside from creating a private chat room, which is too much work at the moment (and would anyway be a waste of a chatroom in most cases). There are other cases where new users use custom flags when they basically want to call the question OT or NARQ (using the specific flag means that it goes to the close vote queues).
According to this answer quoting an authoritative source, as of now, "helpful" is for whenever the user was acting in good faith. Which means that there are even more "wrong" flags that must be marked as "helpful", thus giving us no way to teach the user what to flag.
My proposal is to allow us to write a custom message along with "helpful", which is delivered to the user's notifications inbox (linking them to their "flagged posts" page, which will show the full reply):
For consistency, let us choose to ping the users on a custom decline as well:
There are many times when I'd want the user to read the decline message (especially when it's a user flagging in good faith). In the current system, I don't even know if the user reads the decline message. It is pointless for me to write the decline message in the first place if the user isn't reading it.