One issue is that even with scooping, a substrate swap will be necessary eventually in an undersized "bioactive" due to buildup of organics from waste, minerals from water (an issue even if RO water is used), and possibly helminth and other parasites/pathogens. Even in a not-undersized system, much of the work of what I'd call a real bioactive enclosure (one that can fully process the waste of the resident animals for decades) is done by water that flows through the substrate and then removed from the system, much like in natural ecosystems (rivers carry away organics).
Tossing out isopods is environmentally problematic (they're invasive), so the discarding of such substrate is best avoided as long as possible. It is in fact illegal to release isopods into the wild in the US (without a permit, which won't be issued for this purpose), so no composting/reuse of the used substrate is possible (without pre-sterilizing anyway, which isn't something I'd enjoy doing).
Since the microfauna aren't doing any real work, it can be argued that using them is a complication with no benefit, and so a naturalistic (natural materials and live plants) enclosure has more to be said for it than does a "bioactive" one.
Your enclosure is visually very attractive, though it illustrates how anything but a traditional more utilitarian setup needs to be much larger. Much of the area in the enclosure isn't exactly usable by the snake. As a bit of an aside, I'd reconsider the sharp rocks to avoid any possible injuries (whether acute or from repeated contact).
Just my two cents.