I agree, it's refreshing to have a discussion instead of a pissing contest. Thanks for the discussion.
You're right in saying the bioactive environment allows various inhabitants, that are often seen as bad, to live within the cycle. However, its important to remember that in a balanced system they both live together and are adapted to do so. Healthy animals often have coccidia. It's not a problem though as its kept in check by their immune system. It's only when something else hinders their immune system that it can become problematic. It's important to remember that these animals have evolved in symbiosis with these parasites, to the point where normal digestive function is aided, and even in some cases reliant on this connection. There are reptiles that actually require exposure to adults faeces in order to survive or thrive. Perhaps more than we realize.
As for your other point about the soil, I don't think it really is that rare once it's set up well. And admittedly that's the kicker. I really think that aquarium water is the best analogy. With fish tanks, it's become normal and we'll understood, so the process is easily taught. I don't know why soil can't be the same. It's really not that difficult, and realistically it's much simpler over time than constant sterilization. Once that nitrogen cycle is stable, keeping it going is just habit, or even just timers. If I'm totally honest, my longest running bioactive enclosure is mostly timers, with me just adding leaf litter sometimes and occasionally turning the soil.
The other thing to remember is that these things are adapted to hardship. The plants, soil, animals etc that are part of this cycle are forgiving to our shortfalls as keepers because nature is much less forgiving and regular. I have mister systems and timers for heat and lighting so that it's a regular system that all grows together. Nature is full of droughts, floods, heat waves and such that make our shortcomings generally within reason as long as it's not too extreme or too long. Most house plants are quite resilient, as are most common reptiles. Not that we should rely on this, but it means if your soil pH drops for a short time, it's not the end of the world. And indeed, with a deeper substrate, like with a bigger fish tank, these things are less likely to fluctuate. As a counterpoint, I'd say nature is resilient, and will fight to survive. Our toughest job is to keep from killing it.
It's the one feature of de Vosjoli's book I slightly disagree with. He recommended a soil of 4-6". I'd say the deeper the better. While the deeper soil will get less aeration, so is more likely to become balanced towards the anaerobic bacteria, the depth allows for less fluctuations in moisture, pH and therefore general soil health. I think a soil of around 8-10" is a good minimum to maintain.
Regarding your last point, have you looked at the Biology of the Reptilia series edited by Carl Gans? It's absolutely revealing and I think one of the best collected works on the internal workings of these animals available. They've made online access absolutely free now and I couldn't possibly suggest anything more. I wish I would've had access to it decades ago! Here's the link:
Biology of the Reptilia: Table of Contents - Gans Collections and Charitable Fund
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