"why would Confederate leaders object to slave or FMoC enrollment if it was already being done"
Maybe because what your seeing is a reaction to facts. If it were being done unofficially, this would probably be why you see written documents against it. If it wasn't happening or possible, nobody would be complaining and there wouldn't be any references about abolishing or preventing it. Most military regulations are made to stop a practice, not to prevent actions that have never happened.
Have you ever seen 30,000 people in a Civil War battle? Would you be able to notice 300 of them were black? In the heat of battle would you care? If we use the Battle of Gettsyburg as an example, where Lee had 71,000 troops, it would be like looking for a needle in a haystack for 710 individuals. So, lets use Picket's charge as a round number, 15,000 soldiers; 150 of them are black; stretched out over about, what, 1 1/2 miles. At best you might notice one. Who would make note?
My 1% is a reference not fact, lets drop it to .5%. If a skirmish included Confederate cavalry of 200 troopers, and one of them was black, would the that fact they noticed a black soldier make a big deal to anyone writing a battle report, or would the results of the event be more important? Depends on the writer, and the circumstances.