I will not dispute your claims, because I haven’t read the book in question. I do know that the CSA Congress authorized suspension of HC for shorter periods and smaller areas than the US Congress did.
It is, of course, entirely possible that the commissioners you mention often operated without congressional authorization.
It's an interesting book, albeit hard to read. Martial law was declared and habeas corpus was suspended throughout much of the war and in all corners of the Confederacy. Men like General Hindman abused the powers throughout the areas they were in charge of. Local authorities in the form of Habeas Corpus Commissioners operated at will, and often used their authority to retaliate against business and political opponents. Very little control was exercised from Richmond, and it might be that there was little interest in doing so.
It is, of course, entirely possible that the commissioners you mention often operated without congressional authorization.
There is no doubt that you are correct to some extent. Original authority did come from Richmond, and little or no attempt was made by the Davis government to safeguard the population from their excesses.