I would suggest that portals need anchors at both ends to form a link, a role in which spiritually/psychically active mudokons fill nicely. Abe, due to his development in such skills, is one anchor, some other force or individual is the other. This would explain the behaviour of the majority of portals.
As for the others, such as those Abe can use, perhaps there are historical portal openings scattered across Oddworld which, for whatever reason, have been retained from the days of mudokon glory. Rare and scattered, they would explain those that grant access to secret areas (perhaps past mudokons crafted them in order to fulfil the prophecy?) and important ones such as those in Monsaic, Necrum, and the temples.
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