Stranger was willing, albeit reluctant, to hunt another Steef to save his own skin. In the Art of Oddworld it’s described how Stranger was designed as a character opposite to Abe – with physical brawn but out of touch with his spiritual side. The story of Stranger’s Wrath is Stranger realizing that he can’t run away and pretend not to be a Steef; he has to discover his spirituality and take his place as the guardian of the river. So his earlier willingness to hunt another Steef is meant to contrast with his rediscovered morals later on.
As for Sekto, the only possibilities I can think of are that he would either prefer to pay Caste Raider as he considers him more trustworthy (perhaps he suspected a trap, or as others have said wanted to “keep it in the family”), or that he in fact suspected Stranger of being a Steef or knowing something about the Steef that would have been of interest to Sekto. Note how after his phone conversation with Stranger he ponders for a moment – that’s likely the moment when he considers the potential threat Stranger might be.
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