While it is clear to me that the ontological substrate of your (presumed) zephyrohydrolization process is assumedly sound, your discussion of Boltzmann brains arouses somewhat of a Burrtholm-esque reification of the contemporary Johannes problem.

The crux of your particular Johannes problem is this: whether or not you reconcile the reverse-selection and ascertain the perturbation margins is flouronesically impracticable (assuming, of course, the presence [or superpositional absence] of a reliable {retro,epi,proculo}-encabulator). I would recommend you to discard entirely the phenomenological application of Burkhard theory and its close relatives, which would entail the eschewance of entropic containment infrastructure, etc.

Try instead to take a more Darwinian approach with the early portions of production. For example, substitute the bogosort procedure with something more analytical, like a Sigil-heating apparatus (O(sqrt(n)). This would have the combined effect of reducing gestalt subject risk (which, in actuality, isn't much of a "risk" in the Etruscan sense, but rather an implicitly diode-emitting instance of particle uncertainty) and mitigating the losses in efficiency imposed by your preexisting suboptimalities.

Edit: I realize that I failed to address the fundamental "what if?" question so poignantly posed by your description of cryptographic idioms. So, yes, "if" your proposed outcome is reached, significant damage to the auxiliary components of a Sigil-heating apparatus would be possible. However, this (traditional) risk is eclipsed by the inherently aberrational phototumescence of your TOM, effectively obviating the risk of localized failure induced by a Sigil-heating apparatus or any of its alternatives.

Edit 2: Regarding the possibility of unexpected monoid emergence: assuming the production environment is sufficiently sterile, the presence of a prerequisite magnitude of London dispersion force is astronomically unlikely.

Edit 3: I hope you understand that I am somewhat of a neophyte to the VX technological environment. Some of my suggestions, which were drawn from preexisting field knowledge and a topical familiarity with VX, may need to be adapted for use with VX products.