So true David, My father was a victim of the records lost at St. Louis but after years and years was finally able to recognized. Lucky for me I kept my original DD-214 and have many copies. I know in my fathers circumstance he was required to fill out paper work with his county when released from active duty. So he left a paper trail in this respect.
There still are some ways of confirming Confederate records at times and it depends upon the State as each one is a little different. In your original post it was from a Kentucky unit. When I try and find Confederates from Kentucky sometimes I find some clues in the Kentucky draft registration which can be found online. Sometimes they are simply listed as in the "Reb Army" or in the "secesh Army" Knowing what county the Confederate soldier was from thanks to the draft registration tells me how old they were and where they lived. Once I know their age many times I can find their census records and gain additional information.
The State of Kentucky knew who was who in most cases.