I don’t think there is any mutual respect between Mudokons and Scrabs and Paramites. I think the latter two will normally hunt and consume a Mudokon, whether it’s been excited by the Magog Cartel or has lived a perfectly natural life, free from trauma. Having them act peacefully towards the Mudokons simply removes the element of savage danger that has always intrigued me about Oddworld: nature there is simply goshdarned harsh.
The Scrabs and Paramites in the Monsaic Sanctum, in my opinion, are either being controlled by the Mudokons’ psychic powers (maybe even possessed), or else have actually been tamed.
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