Daniels - The tables come from performance. Training paces are for a well trained athlete. If you are not well trained, your paces will be off even if your performance fits one of the table values. In a similar way, if you look at the IAAF points table, you will probably find that you "match" the table across a few events. Endurance people have higher values at longer races, speed people have higher values at shorter races. Daniels translates this race performance to training paces for specific types of workouts. VDOT is just a number (like the IAAF Points) to give you to a reasonable set of training paces for your level of performance. Really this keeps you from getting out of control as most people train too fast if left to their own devices.
Peaking - Read some Lydiard on this. He does a ton of short "sharp" sprints near the end of a cycle. This increases the efficiency or neuro-muscular effect at high speed, but cannot be sustained for very long. Long steady running can be sustained. So you get strong first, then you get fast. Viola, you are peaked. I agree that there is a large mental factor here also, but the body must be ready to run fast. Often this helps the mind to be ready to run fast. It's circular. Feel the flow, Happy.