You put <num> around the numbers, to allow people to isolate this
sort of phenomenon? That would seem sensible.
I meet something similar to this in a born digital context where
the text must be made available either using US/UK convention
for decimal separators or French convention. I use <num> to
let me work the needed magic. But thats just modern conventions.
By the way, when you say "(6) if a novel glyph is used or or a
heavily-weighted character is misused
in the separator role, invent a new PUA character." presumably you
also document that using the TEI mechanisms?
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