Exactly, these orders to organize battalions of sharpshooter, were not attempting to form battalions of 3 to 6 companies of "Snipers". They were being organized for another purpose. They were taking some of the best soldiers in each brigade, and that included their shooting skills, and using them to create a front line buffer zone. Their skills as skirmishers usually held the enemy probing attempts at bay and screened the main battleline until the concerted push was actually ordered by the enemy where sheer numbers would force these skirmishers to withdraw back to the safety of their Brigade.
Did these skirmishers take shots at targets of oppertunity? Yes they certainly did. But they weren't armed with special rifles for that purpose, nor was that their primary military purpose. the marksman armed with the special rifles were employed as you said they were at Fort Wagner. It is difficult to seperate the fact from the myth of the Civil War Sniper because of this definition of terms like Sharpshooter and Marksman. Actually Marksman is the more correct term, in my opinion, that was used to designate a Civil War "Sniper"