It was recently pointed out in TIL that Mississippi didn't ratify the Thirteenth Amendment until 2013.
So I was looking into the whole issue and it occurred to me that we have an official order of admission. So why didn't they take their place at the end of the line?
From the point of view of the Federal Government, the Southern States never left the Union and there was no such thing as The Confederate States of America. Same goes for other nations. No country recognised the independence of the Confederacy.
If you look at official correspondences from the Federal government, they always referred to it as “the supposed” Confederacy.