Yes, I agree that Brutha would have learned more skills as he spent the years copying out the books. I was speculating as to which ones he would have learned first, and what choices he would have made. If the experience of the scrolls makes it possible for him to read and write, then all he has to do is practice. (It's also the story of a young man discovering literacy.)
Having known a man who had eidetic memory, I find it fairly easy to accept Brutha's memory, especially as a Discworld fact. I'm not sure how Om had any influence on the Library demonstration. Brutha had the eidetic memory from birth, long before he ever heard Om speak. In one short scene Brutha rescues Om from Didactylos by explaining that the tortoise was setting up a sting by pretending to fail, and not so incidentally claims the tortoise as his property; Om did speak to Brutha then. But during most if not all of the memorizing scene, Om isn't even present. Simony was off fetching Om from Brutha's room.
Canon narration says that books interact when they are shelved too close together. This is a Discworld fact, unrelated to our reality. While the books in Ephebe are probably not magical, they don't need to be magical to interact. Brutha's experience of having them interact in his mind so quickly is a fast way to show what normally happens more slowly in our reality when we read books and think about them.
While SG can be read as a treatise on fundamentalism, it can also be read as a history of the Enlightenment, when ancient knowledge from the Mediterranean cultures (not just Greece) became available in Europe and sparked huge social changes.
On a metaphorical level, it can also be read as the story of one individual who becomes at least somewhat enlightened in both the eighteenth century sense and a Buddhist sense. Brutha listens. That verb is repeated, over and over. Brutha listened. Brutha heard the voice of his god, argued with his god, even threatened his god, and demanded that his god be worthy of his belief. It is a demonstration of how a human being can shape a god. As I understand it, enlightenment in a Buddhist sense involves becoming aware of your mind and seeing how it works. Brutha's mind begins to watch itself as he walks the desert.
The imagery of light fills the book. Lu Tze's name, which sounds like "lucy", resonates with Latin "luci-" as in "lucifer", the light bringer, the son of the morning. The brightest one. And the one who spoke - hissed - to the innocent in the garden. (His life was probably saved by Lu Tze, who may have put a pile of compost where Om was going to land. Lu Tze moves mountains and brought one to Brutha.) The Citadel is dark, and most of it is underground. Light wells bring in controlled amounts of light; the rhetoric is twisted by Vorbis so that the idea of bringing light in so that nothing was hidden became a horrifying pride in the torture chambers. The harsh light of the desert burns away most illusions. The Citadel is dark, but Ephebe is built of white stone that reflects light and makes the city very bright. One of their strongest defenses uses light itself as a weapon.
Not that Ephebe is perfect. Nothing in this book is perfect except Brutha's memory, and that has some locked-away parts.
We see flaws in Ephebian culture. We can see flaws in the Ephebian science in the scrolls Brutha remembers. The Ephebians, as their culture continues, will no doubt continue their scientific investigations and correct the errors. Eventually, some of the scrolls Brutha copies out will be discredited, particularly the ones that try to explain the observations of natural phenomena (natural philosophy). That doesn't make them useless; it makes them part of the history of thought.