The Head Coach can say whatever he wants, and if he says it respectfully, an official should show the curtesy of listening. Beyond that the final judgment is exclusively the official's.
I'll without question agree with that, but given the situation here, and a "strict" reading of the applicable definitions, and related rules, and the incoming substitute never really "assumes his position" when can we flag A for having 12 on the field? The referenced AR seems to fit perfectly here, except it specifically applies to team B, and the result we have here is that team A has 6 potentially eligible numbered bodies on the field for an extended time before one of them finally leaves as A is getting into pre-snap positions.
Can we read the AR 9-2-2-IV to also apply to team A someting like:
IV. Between scrimmage downs, one or more Team
A B substitutes enter the field of play. Before the snap for the next down, more than 11 Team
A B players intentionally stay on the field of play as long as possible (more than three seconds) to disguise the
offensive defensive personnel, the type of
offense defense and the
needed pass coverage. RULING: Dead-ball foul on Team
A B, illegal substitution. Penalty—Five yards from the succeeding spot (Rule 3-5-2-c).