I don't see the books as a reference to magic. Think about it normally, without water you can not have wind, and without wind fire can not exist. It is that simple.
Actually, it's yet simpler I should think. What's written in that book is probably some old, or maybe earthbound, writing or poetry. It's not some concrete book of science or magic. All it implies is that, to observation, wind and the waves are connected, which may simply be an echo of old superstition. And the fire is yet easier: it does not say anything about the connection between wind and fire, merely that one makes the other dance. It is imagry, pure and simple. Some scholar at Zeal likely thought it a quaint thing and used it as the key to the secret room.
In all reason, though, CT is working on fragmented and mingled western/eastern philosophies, and CC attempts to reconcile it all to some extent. Fire, Water, Earth, Air... that is called the Aristotilian world-view (different than our one now, which I suppose could be called Democritian.) CT took that standard, and often cliched array, and turned it about a little. They kept fire and water, but made Earth deeper, and Air higher. In some respect, if you think about it, even in the Greek view, who owns the earth - and by that I mean under the earth, not upon it. It is Hades, a very shadowy lord. And what of the airs? Those, if you expand upon them, reach to the heavens. Thus Heavenly/Lightning is a glorified 'Air' and Shadow a glorified 'Earth'. Also, ideas of Heavenly and Shadow likely tie more into Eastern philosophies. This also, likely, accounts for Shadow being a mixture of the other three, rather than an equal of the other four constitutive elements, as it would be in the west. Now, CC attempts to change this a little. It removes Heavenly and Shadow from the four, giving them pre-eminent places apart. The four now are the standard Aristotilian elements: Red for Fire, Blue for Water, Yellow for Earth, and Green for Air... with some allowances, admittedly. White and Black are now set apart, more powerful than these, or at least unique - neither has a 'field' element, for example, and they are each representative of the most powerful warring sides... though not neccessarially as one might think. Serge, Fate, Lynx, and the Time Devourer, are all white/black, though Serge is both white and black, and the Time Devourer is white, proving that black does not imply evil. So Chrono Cross is perhaps the fulfilment of what is shown in Chrono Trigger, replacing the two missing elements.
Another theory on the matter, however, is that Green and Yellow are rather a mingling of the old four.
Now through all of this, I am inclined to think that, intent wise, there is no actual good or evil attached to black or white, Lightning or Shadow. They are just opposites. This is not like the Force, with a Light and Dark side, and one cannot be tempted by Shadow (different from the shadows) any more than by Lightning. Both are symbols of power, and both can be used evilly. However, it seems to be that Shadow is a little more difficult to use, more secretive and, if the quote about it being a mingling of the other three is right, extremely rare. Thus it may be thought that only those that study for a long time, or are born apart, can make use of these, and often these unique or secritive people are themselves evil. Thus it is by parallell, but not by cause, that a Shadow innate might be evil. After all, one must remember that Magus was Shadow innate and, while grim and morose in his youth, he had commited no grave atrocities so as to label him evil. It likely works like the old system of Humours, where an excess of Melecholy Humour made one, well, melencholy and morose. Bile, and and the like had other effects, and by this the middle ages people attributed tempers to people. An excess of one put one out of balance, and gave them a temper far to one side. This magic system is likely of a similar sort. Thus a Shadow innate may be grim and sullen, a Lighning innate more bright and cheerful and prone to heroics, a Fire innate quite-tempered, and so forth. It may then lend greater influence to a certain good or evil side, but by no means precludes a single allegiance.
