I agree with you, of course. There are reasons why things are the way they are. However, people like Crowley, for example, took those same ideas and subverted them, making the normal rules not applicable. Things like the Great Whore of Abominations and Beast 666 don't mean the same thing today, in the specialized circles dealing in magic, as they did previously. The GD not only followed some established traditions, but also made up new ones. It is also important to separate fact from fiction.
For example, the Salem witch trials are a complete invention. Not that they didn't happen, but the root of the problem was a property dispute fed by paranoia, no magic was involved, despite mainstream traditions and the tourist trap Salem has become today. The most well-known depiction of the Baphomet is a lie, an accusation made against the Knights Templar. Earlier, the symbol of the goat appears in the bible, in which the animal was laden with the community's sins and left in the desert. Even in the book you mentioned, "Dogme et Rituel de la Haute Magie," says of the Baphoment that it represents the "sum total of the universe," bearing the words
solve and
coagula on its arms, representing the Great Work.
Point is, the occult was hidden for most of history because of the knowledge that popular views would misunderstand certain symbols. Normal rules of popular perception don't apply. The average person is perhaps the worst judge possible of what constitutes black magickal symbols. Pan has been mentioned previously in this thread; the popular view of the red, horned Devil is probably political propaganda.
Aleister Crowley said:
This serpent, SATAN, is not the enemy of Man, but He who made Gods of our race, knowing Good and Evil; He bade 'Know Thyself!' and taught Initiation. He is 'The Devil' of the Book of Thoth, and His emblem is BAPHOMET, the Androgyne who is the hieroglyph of arcane perfection... He is therefore Life, and Love. But moreover his letter is ayin, the Eye, so that he is Light; and his Zodiacal image is Capricornus, that leaping goat whose attribute is Liberty.
The Lord of Matter is a way of shaming people, intimating that anything physical is an unholy blasphemy.