I feel as though rather than it being specifically Mudokon bones that were coming from Rupturefarms it might have been just any bones in general from the livestock at the meat processing facility. When Rupturefarms shut down this was when they didn't have a supply of livestock bones so they resorted to digging up a Mudokon burial ground and found that these Mudokon bones had, "Twice Ze Flavour."
This still doesn't explain how well set up the Soulstorm Mining Co. appears to be, so perhaps they were just doing it to a lesser extent, since in Exoddus we see them trying to expand into the Mudomo/Mudanche Vaults?
Either way, I like the idea of Abe's good intentions having these kinds of consequences.
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