Possibly so - the essential attributes of nationhood are a topic discussed with respect to international relations and the proliferation of "micro-nations" these days.
The the case of Biafra. Nation-state or not? They were diplomatically recognized as such by a few of their neighboring countries, but they failed to enforce their borders against the sovereign authority the rebelled against.
"The lack of a Supreme Court is not especially troubling considering they were at war."
I agree. The United States did not have a Supreme Court until Congress created it by legislation following the ratification of the Constitution. The difference being, the confederate constitution called for that court and the confederate legislature never created it. That's why I used the term "fully functioning." If you have not read it, I would recommend The Cause Lost by William C. Davis. It is still in print in paperback.
"The CSA certainly had reasonable control exercised over its territory until Union forces began invading in earnest in 1862 - with the possible exception of sparsely inhabited and remote areas of western Virginia. But then the same thing can be said of the US itself, which was unable to prevent CSA incursions into Indian Territory and New Mexico Territory - or, for that matter, the eleven states which seceded. By your definition, the USA itself in 1861 has difficulty meeting that definition."
The point which I was making was especially in regard to Kentucky and Missouri. The United States had internationally recognized boundaries that were from time to time violated (i.e War of 1812). To maintain territorial integrity, borders need to be defended, and they were. In the case of the confederacy, they claimed territory they had no control over at all.
I have Davis's "An Honorable Defeat" - an outstanding book, by the way. But I haven't read that one.
But from what I have read of Davis, I sense that if you put the question to him whether the CSA fulfilled the basic criteria of a nation state by 19th cenbtury standards, it be hard for him to say they didn't. But maybe I'm misreading him.
Given that the CSA was at war almost from its birth, it'shard to nick them for failing to establishing every body called for in their constitution. Perhaps not "fully functioning" by their own announced standards but certainly by any reasonable standards for a functioning government. The government departments not related to war obviously stayed atrophied in some fashion while the war was still on.
In the end they could not uphold their sovereignty and their claims against the superior might of the Union. But that doesn't mean that for much of the war that they didn't meet the basic tests of nationhood, recognized or not by foreign powers.
I don't know what more to say about Kentucky and Missouri. I think it was unwise for Richmond to extend such hasty admission to both states when neither had the clear consensus for secession that the eleven "real" Confederate states did. But then the US itself has a similar difficulty. In 1861 Abe Lincoln claimed an executive power that reached from the Reio Grande and Key West to the Canadian border, yet his writ did not run south of the Potomac more than a few miles.
Eventually Lincoln made good those claims, but it cost him 380,000 dead and untold millions to do so. But being beaten doesn't mean the CSA didn't meet the requirements of a nation state, any more than the Dutch or France were for being conquered by Hitler (which is not suggest any equivalence between Hitler and Lincoln - I know I probably got Stand Watie all excited there for a second).
But there are many cases of nation states claiming territory they don't have effective control over without their essence being called into question. That's certainly the case for the European empires of the day. The King of Belgium claimed the entire Congo in 1885 but his control was effective over a few square miles around outposts like Leopoldville.
In modern political science there's been discussion over Africa states facing the same difficulty as King Leopold and wondering whether they meet the critria of sovereignty at all. I think there's a better case to be made against such states than against the CSA for the first years of its existence.
But I think it should be clear that, however I may admire the valor of southern leaders and fighting men, or certain attributes of southern culture, that I'm glad the South lost, and that I think secession is at best a very dubious doctrine. All my (Illinois German) ancestors worse blue. All I'm doing here is recognizing that, like it or not, the CSA managed to set up a functioning nation state of sorts (with pretty remarkable popular support) during its brief existence.
The several Indian tribes have long been ruled 'nations' by the US supreme Court, and treaty and diplomatic relations with the US prior to the war. The following Indian nations all established treaties with the Confederate States:
Creek
Choctaw
Chickasaw
Seminole
Peneteghca (Comanches)
Wichitas
CadoHadachos
Huecos
Tahuacaros
Anadaghcos
Toncawes
Aionais
Kichais
Shawnee
Delaware
Neconi
Taneiwe
Cochotinca
Yaparihca (Comanche)
Great Osage
Seneca (of Sandusky)
Shawnees (of Seneca)
Shawnees (of Lewistown)
Quapaw
Cherokee