But if so, why would there be reports of 'cut and paste' AC3 audio tracks into a .mov container working?
Because a Quicktime MOV container and an MPEG-4 container are not the same thing. There are strict rules on what the public streams in an MPEG-4 container must contain.
The Quicktime MOV container has no such rules, and permits you to jam all manner of crazy data into it, including an AC3 audio track.