Does not sound like there is anything missing in the story to me.
The inexperienced acting center manager didn't know what he was doing, he is a hard ass, and dishonest...I have had managers of this type.
The directive to not sheet miss-loads as missed might have come from the prior center manager who was recently transferred. The acting center manager may not have known (or may claim ignorance) about the directive not to sheet. The instruction to sheet with separate DIAD is the smoking gun that management was trying to bury them. We had the same directive (no sheeting as missed unless directed to do so). I sheet them as missed and send them an additional text stating that I am doing so.
The acting center manager seemed not to know the driver told his on car that he would probably not be able to run them, and initially seemed unaware the driver also notified the center.
My question to the OP would be...
When you sent in the miss-loads did you initially respond Y to the prompt "can you deliver"? If so, the driver still informed his on car later on. The on car may deny meeting the driver to take the school pkgs. to avoid a grievance over that issue.
Sounds like the management team is going to try to deny that a "don't sheet till instructed to" policy existed. the OP should be finding other drivers immediately that will state they were instructed to do the same.