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No, I think he means that the Mudokons you see in captivity at the end of AE appear to be in the same cell seen in the FMV where Phleg is "employing" Mudokons for the Soulstorm workforce.
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If that's true, then it's not in the brewery but rather out in the desert somewhere. If you look closely though, there are enough subtle differences to imply that it's somewhere else. I presume OWI simply used the same CG model and made some small tweaks to it.