There is a lot of relevant information that he left out of the first four chapters, much of it things that run counter to the thesis of his book. And I honestly can't say if it's because he's found ways to rationalize away the information, whether he's not aware of it due to being unwilling to consider certain possibilities, or if he's deliberately leaving information that doesn't fit out. Any or all are possibilities.
One possibility is also an example of how a modern point of view and a focus exclusively on race can cause him to miss certain possibilities. We have 150 years of centralized government in the US, and it's common for people like Levin to project that back when evaluating Confederate actions. The way he focuses solely on the national Confederate military and excludes nearly all discussion of state militias or state actions is a prime example. The Confederate States were set up as a more decentralized system with more state power, despite some wartime measures by the Confederate government to exercise more power due to wartime pressures and challenges. State actions must be taken into account when considering the topic of black soldiers. States were the first to accept armed black men into their military, primarily Louisiana in 1861 but also the area around Mobile Alabama in late 1862 (this is the group Maury wanted enlisted into the CS army but was turned down). You will not get this history right taking a top-down view of the Confederate political and military system. Add to that a focus almost entirely on slaves with no real consideration of the free black population beyond a few mentions, and you can see how relevant facts are omitted from consideration.
Purely from what you say here I don't think he's missing anything or projecting anything by focusing on the Confederate nation. A State is not the Confederacy. Literally by definition. They are a piece of what made up the Confederacy. In most topics regarding the Confederacy, and its military, people do the exact same as him and focus on the official Confederacy and its official actions (including its official military). Nothing surprising or different compared to the majority of focus on such topics.
This doesn't mean what States did on their own isn't important, but objectively it's far less about the "Confederacy" than it is about that specific Confederate State.
"Add to that a focus almost entirely on slaves with no real consideration of the free black population beyond a few mentions, and you can see how relevant facts are omitted from consideration."
I'm curious on the full scope of that, but again this wouldn't be surprising as well. Why would you
not expect a focus on Blacks on the Confederacy to mostly focus on slaves when
96% of the black population in the South were slaves. Specifically in 1860 the to be CSA states had 3,521,110 slaves and 132,760 free colored.
This thread is really pushing this book to the top of my list!
That's part of the whole argued "Black Confederate Myth"... it's not that Black Confederates didn't exist, it's that one side wants to overly exaggerate an extremely small portion of the Southern Black population while under-emphasizing the vast majority. It's not even about personal interest, often people find the rare and outlying cases more fascinating and focus on it, but it's disingenuous when people falsely exaggerate that representation. Likewise if someone is looking at an objective look of the overall concept of "Black Confederates" you simply have to expect them to focus mostly on slaves (though not exclusively of course).
I think that's the point, there are multiple views on the topic
1. Top down view of Blacks and how many who were involved in the Confederacy can be reasonably called "Black Confederates"
2. Bottom up view focusing on the rare outlying cases of genuine and high confidence Black Confederates
Neither are implicitly flawed, but both should be considered in their context.
#2 would have to be understood within the context they were extremely rare and a small portion of the Black population within the Confederacy, much like say focusing on any topic about free blacks in the South in general. It's important and can be valuable, but should be understood and not represented that this was a common or typical experience.
#1 would be an overall look of the typical experience and perspectives of Blacks in the South and their involvement with the Confederacy. Slaves being 96% of the Black Southern population means that will implicitly be the focus. If that is indeed the focus of this book then that's potentially quite refreshing since usually the focus is on #2. In studying an anomaly under a microscope and sometimes deceptively exaggerating that microscopic view as more than an anomaly.