In our 5 man crews, the R & U count A. We also alert the wings to covered potential receivers.
IMO discrete signals are fine, obvious signals such as a hand on the head and pointing to a covered receiver, or pointing to players as you count them with your hand on your flag are also fine. If a coach sees this and has to call time out or another action to check or correct it is on him, not me. His assuming what you are doing is on him. I consider this a form of preventive officiating, allowing a team to correct it's problem. Also, if I am wrong, it is not my problem. To tell a coach what you are doing places it on you.