We have strayed far from the original topic of this thread.
In my not so humble opinion, your criticisms are apt. Creatures, monstrous or otherwise, have gotten short shrift in Tekumel publications. I don't think Barker had much interest in natural history. Consider the remarkable absence of creatures as symbols in Tsolyanu. Hardly any legions have creatures in their names (the only one I can think of is Vrishtara the Mole. Only one or two clan names have anything to do with animals. Only two deities have creatures as important symbols (Ksarul's beetle and Sarku's worm) but neither are there for their qualities. Many deities have one or more monstrous, non-human aspects, but very few of these, if any, correspond to creatures otherwise known. Compare that to the way that pre-industrial human societies used symbols of real and mythical creatures in their art and culture and literature, it's a strange omission. Cats and dogs are present in the Five Empires, but even these never, or almost never, appear in the novels.
Most of the creature text in the Bestiary is taken directly from the original Empire of the Petal Throne game, with no elaboration, so you might judge them by the standards of 1975. In EPT, Barker mentions "Saturday Night Specials", referring to "unique creatures dwelling here and there in the Underworld guarding especially valuable treasures or other items." Not exactly an ecological mindset.

regarding the Haqél, the large predator in "deep lakes and streams," I think there "stream" is being used as a synonym for "river" and is not meant to imply a small watercourse. So in my Tekumel, Haquel are found in the navigable portions of rivers, with big ones only in the lower reaches of the big rivers.
regarding the Nenyelu (2-5 m long eels with a neurotoxic bite, rudimentary hands and arms that can throw rocks, and high animal intelligence). Who knows? Maybe a wizard did it? Since the entire ecology of the planet is artificial, we don't have to restrict ourselves to natural evolution to explain the origins of species.