Jeff, the way I read Travis' reply was the tolerance is +0, -X, meaning you can be under by a reasonable amount, but not over by any amount.
Here is the thread you mentioned:
http://classracer.com/classforum/showthread.php?t=25533
In that thread, Travis made it pretty clear that if the spec was 1.5:1, for example, that 1.50:1 was legal, and 1.51:1 was not.
Yes, it is up to the engine builder to determine the actual rocker ratio as the engine is being run, and the racer is responsible for it.
Engine builders are human, as are racers, and they make mistakes. Without naming anyone, it has not been that long that a very well known racer was DQ'd from a race for this very reason, and his engine builder is extremely well known as one of the very best in the business. Both parties involved are stand up individuals, and the size of the infraction would not have made any difference in power. All they did wrong was to not check for lift at every single rocker, so the tolerances stacked up and they got bit.