While all of this is interesting, these discrepancies don't really mean much. Whether or not one chooses Holmes or Cook to begin with, eventually one can only really go with Cook because he is the one who provides saves for higher level characters.
Nonetheless, Holmes does give us a fascinating take on what a Saving Throw is:
Even when a magical spell has been properly thrown, it does not always work. Anyone subjected to magical attack rolls a special die to see if the magic took effect (see below). This die roll is called a "saving throw" because if you roll the correct number (given in the chart below) or any higher number, you are unaffected or "saved."
Note those two very intriguing words: magical attack. Indeed, when he describes Dwarves, he states:
They are sturdy fighters and are especially resistant to magic as shown by their better saving throws against magical attack.
Given the fact that Dwarven saving throws are better across the board than any other class, this means that every time a character makes a save it is against a magical attack.
In other words, the bite of a giant spider and the breath weapon of a dragon are not natural — they are magical. This throws a gigantic wrench into the assumed naturalism used by Gygax, Arneson and their progeny (like myself). It also adds credence to the notion that the Dungeon is a magical, otherworldly place that has its own agenda.
This view, however, doesn't stop me from asking a few questions and making some assumptions from a naturalistic POV. Ignoring the demi-humans for a moment, Clerics have the best saving throws to begin with. The non-spell casters (Fighters and Thieves) have the worst. If one looks at the name-level of each of class, however, while Clerics still have the best saves, Magic-users have the worst.
This seems to indicate that being associated with divine magic consistently makes the Cleric more resistant to magical attacks than any other class. In contrast, while it initially gives them an advantage over non-spellcasters, being associated with arcane magic makes Magic-users more susceptible over time to magical attacks than any other class.
This reinforces the idea that the arcane magics of the ancients, while powerful, are dangerous. It also continues to suggest that civilization has made a move away from paganism towards some kind of Christianity — being strongly associated with the Church helps protect one from the nasty magical effects of the pagan (and ultimately evil) ancient civilization that still plague the world.
This pattern also holds true in context of the demi-humans, where the one race most closely associated with arcane magic (the Elf) is the most vulnerable to magical attacks. It begs the question, however, why demi-humans are overall more magic-resistant than humans.
One simple answer is to assume that the ancient civilization so closely related to powerful arcane magic (and the turning away from God to produce an evil slave economy) was a human civilization. The very close association humans had for so long with such powerful arcane magic made them all far more vulnerable to magic attacks than the demi-humans — especially those that never dabbled in magic like the Halflings and the Dwarves.