One thing that comes pretty clear working through the THS sourcebook, even a mild application of the tech there would just cream a blunt force like the Kafers (who AFAICT don't truck with biotech).
The Kafers are designed as an adversary for humanity in 2300.
If you mix transhuman ideas into your 2300, I'd suggest you apply it to everyone. It'd probably make the Kafers more interesting.
For instance, what if the Kafers are actually the "dominant" form of a once much more advanced alien race that ran into a lifeform so advanced it faced extinction (like they did something that actually ticked the AGRA intelligence off). However, the species realized that it could survive by flying under the AGRA intelligence's radar by being ... unintelligent. The "part-time intelligence" of Kafers is actually a stealth technology to evade the AGRA's senses, which don't work in the same ways our do at all. It identifies individuals and species by their "intelligence." So enemy's intelligence had a certain "scent" and the AGRA would hunt it down. The engineered Kafers were usually too dumb to qualify as "intelligent" so the AGRA contented itself destroying the remnants of civilization on the Kafer homeworld, then departed.
Tens or even hundreds of thousands of years later, the Kafers have created a kind of civilization despite all their handicaps, yet the original life-form's DNA is still encoded into the Kafers, perhaps with a highly sophisticated symbiotic lifeform like http://en.wikipedia.org/wiki/Deinococcus_radiodurans
that works to preserve the original Kafer genetic code through all the biological stresses of the world and makes Kafers resist Transhumanity's attempt at wholesale modification.
However, this original lifeform is still encoded in "dormant" gene pairs hidden deep within the Kafer genome. It's called forth by certain stresses on an unconscious level which release certain pheromones which activate the "recessive" form of Kafers, which proceed to produce children who are of the old species template who then breed true. Transhumanity mucking around in the Kafer genetic code sets off one of these "genetic booby traps" ... probably thousands of times, but usually in labs so nobody notices except as scientific curiousity. Eventually someone does it with a Kafer which has exposure to a larger population. This makes the Kafers revert back to their atavistic form, a much more capable, dangerous lifeform, yet perhaps one that is easier to write adventures around.
Of course, the AGRA intelligence may have never forgotten its foe (since time doesn't pass for the AGRA in the way it does for us) and their utterly alien perception might lump humanity in with the Kafers as "enemy." After all, to the AGRA we're nothing but bugs. If you see ants coming to your shed and fighting the termites who are eating your shed, you're probably just going to exterminate both of them.