Yes, the Hork-Bajir were designed, but they were designed 10000 years ago (I think), but the moment they are out of the lab, they become subject to typical evolution.
That's plenty of time for behavioral changes to start cropping up, especially in a species that learns: they aren't brilliant, but they could figure that out. It might not be a great advantage, but I'd wage it's enough to persist in the species.
I'm not saying it would, for canon's sake we can say it didn't, but again, I don't think it's good to use limited evolution as a blanket explanation to uniformity of Hork-Bajir
And let's face it, the Arn can't engineer out competition any more they the can engineer out intelligence. The former is almost a fundamental property of life forms. You'll have mutants for that just like you have seers
and we are now way off base, but I like it