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.
Davis did everything he could to permit excesses by the pretended southern national government. Per their written constitution, there should have been a counterpart to the Supreme Court. Davis never appointed anyone to that body, so their were no legal restraints on the southern government.
It was common for southern officers to use US uniforms on reconnaissance. That was how Jackson got shot by his own men.