If you could determine with 99% accuracy the exact genome of a child by their parents genomes alone, would you be able to optimize humans across given a relatively small set?
Also "wild genes" - particularly those of the Fremen - producing unexpected results (ex: Leto II).
The Bene Tleilax though, they're probably making solid genetic projections.
This leaves aside the more important question raised by the scope of the Dune universe, which is defining what 'optimal' would even mean in such a world. Traits are only optimal or sub-optimal relative to an environment. Being smart and not able to move heavy objects would doom a medieval man, but being stupid but strong would hamper a modern man. That's a facile example and you'd be more likely talking about weakness to certain pathogens, dependence upon particular physical environmental needs (oxygen level, caloric availability, body temperature control efficiency, etc) though, really. If you're going to be planet-hopping and galavanting across the universe, what is optimal in one place can kill you in another and vice versa. The myth that there is a 'strongest' state is just that, a myth.
In genetics, diversity always wins. Flexibility and complexity always wins. Being mediocre at everything is a far greater survival trait than being a master at one is if it means you are a total failure on another count. Living things can only fail once.
Furthermore, one can now ask if the more perfect specimen for a given environment might be a chimera: this genome for nervous system, that genome for leg muscles, this other genome for internal organs, etc.
But your main point stands. The Dune series presumes that such a thing as breeding a superior human is not very difficult to manage on the scale of mere centuries. I am not sure how even define such a thing. And I rather doubt such a specimen would breed true with a similarly superior specimen.
Writers that take your approach - it’s all made up so I’ll just make up new rules whenever so feel like it - are rarely satisfying because the reader can’t trust anything or reason about the setting or the characters choices.
This is the problem with J.J. Abrams approach Star Trek and Star Wars. He seemed to take a special glee in arbitrarily violating established conventions in the settings with respect to things like how Warp Drive and Transporter technology work in Star Trek.