The way the secret society evolved, even with offshoots, speaks a disconcerting and disturbing history... sometimes protective of the freethinking heretics and serious scientists and artists, this occurring in the heydays of the Inquisition, absolute monarchy, and noble or wealthy houses seeking power. There was a problem with the way money and wealth was flowing, with the price of power for both Church, monarch, and noble being indebtedness to those in orders like the Knights Templar, and desire for the wealth of other areas and groups like the Cathars, the Medicis, etc. Between the lust for power and autonomy over people's bodies, minds, and souls; and the greed for wealth in order to maintain this power through standing and mercenary armies and wars, the secret societies would have had to resort to very arcane, codified, and obfuscatory smoke and mirrors both to keep its members alive but also its purpose, to protect, save, and hide true scientists and classical learning, as well as those the Church considered heretical or overly free thinking. Esoterica, arcana, alchemy, sacred geometry, secret rites, codes, and even perhaps a kind of spiritual belief system were all involved in the society's schema and modus operandi, though probably not all at once or in the same intensity or density, depending on the place and time and the people involved.
Over the years, the secret society devolved, due to the weakening of the monarchy, revolution, and the formation of Protestant or dissident religious factions. As the monarchy lost power, if not its name, and the Church lost its military and state function, the secret societies also lost their former raison d'etre, no longer needing to protect or hide the geniuses carrying the torch of rational science and free thinking. Thus, we see the rise of the esoteric, the arcane, the alchemical, and the rites to become ends or means in themselves; and members and their satellite groupies, mostly artists and musicians, became more interested in their own individual success and wealth. Yes, we see some very marvelous and interesting associations forming between artists, musicians, writers, and politicians, more and more interwoven with the theosophical, spiritualist, occult movement. At that point it gets nasty, anti-Semitic, more and more Aryan, Euro-centric, and difficult to defend or assess. That's why people like Plantard and others had to invent a dynasty and a way of deflecting their ties with Nazism and other insider schemes for gaining wealth and power for their members. The Bush family connection shows a little how this has worked in the latter half of the twentieth century.
Now, as you say, the rules or processes of alchemy, with its specialized and arcane language, can indeed be used to describe psychological and spiritual transformations in individual humans. Jung spent a lot of time and effort doing just that. I suppose it's fine to look at the metaphorical and symbolic aspects of the old "science" as interesting and informative in that sense. But poetry, drama, and prose can do the same thing, along with music; and so can the teachings of any mystical or spiritual tradition.
What's important, in my view, is keeping a balance between the reality and the mystical, and to keep the physical history separate from the psychologican and spiritual. Not to do so invites the same mistakes and perils that gave rise to Nazism, and is giving rise to the vicious social darwinism and corporo-fascism that neocons and Christian fundies are perpetrating on this country and the world... and these powerful people belong to the secret societies that many want to romanticize or demonize, instead of taking a good hard look at what's really going on.