Why would a lowly corporal be apart of a conversation involving classified information between the battery commander and the commander of the submarine on a secret mission? That signal would be useful in the wrong hands and Corporal McClarin would not have a need to know since he was a mechanic and not a crew member. I'm not saying there was no signal, we just do not know what exactly that signal was. Also, there were at least two loaded whale boats from the Housatonic over the wreck site and the U.S.S Canandaigua was once credited with running the Hunley over any one of them or others could have used a blue light. The signal could well have been a more practical Coston Light with the ability to code a series of lights specific to the Hunley--- we simply don't know.
As for the operational control of the Hunley...it's track record says it all, I don't care how easy Hunley thought it was- it killed him and it killed Dixon and his men too.