Having followed qntm's work since Fine Structure (2006), he's really improved since then. He got a lot better at character writing with Ra (2011).
I think it's largely a matter of intentional practice. I think that some sci-fi writers don't prioritize honing that skill, since they just want to build a cool world and the story is a way to demonstrate that.
I have never heard of that book, but a quick Google search reveals that the author is in the process of "releasing version 2". Refer to the previous comment for my opinion on that matter.
In addition to the content licensing, it was released as serial web fiction presented in a wiki. Serial fiction usually benefits from significant editing to fit the structure of a novel.
I think you read novels by bad writers, who happened to be engineers.