This is moreso what I was driving at - i know the rule (NCAA is similar) but I don't understand the logic behind it for this very specific case. The rules also appear to be in conflict - FC rules say R can't advance, but scrimmage kick rules say if they catch/recover behind the NZ, both teams can advance. Usually in situations like these, we see a 'if not in conflict with other rules' statement. I don't see anything that says FC rules trump scrimmage kick rule in this situation.
The point is, when B gives a FC signal, Team A relaxes. They know they don't have to tackle anyone. Letting B advance after a signal gives them an advantage.
Let's say the kicker pops the kick straight up and B signals for a FC and catches the ball 2 yards behind the NZ. Team A is going to relax and not tackle him. That's why the ball is dead.
NCAA actually changed this about 10 years ago. FC signals behind the NZ were ignored. Now the ball is dead no matter what.