Major reason had little to do with shooting skill.
To win, the South had only to avoid losing. They therefore, especially after Gettysburg when most of the casualties occurred, normally fought on the defensive from behind fortifications. When Lee first took command, his troops called him Granny Lee because he was always making them dig in. It is to be expected that assaulting fortifications will be more costly than defending them, that's the whole point of digging in.
Due to the more constricted terrain, there was less room for maneuver on the eastern front, and much more trench warfare than in the west.
Many exceptions, of course, to these generalities.
The South of necessity had always mostly fought defensive battles up to Gettysburg. When Lee against advice from all his subordinate officers, got his nose wide and PO, attacked a superior enemy in defensive positions. The battle cry of the Union troops at Gettysburg was “Fredericksburg” from battle of same name where they suffered huge losses when situation was the reverse.
The actual trench warfare you reference did not come into being until last months of the war around Petersburg, VA.
I think the best defensive Confederate General was Joe Johnston, where in the Hundred Days Battle in Georgia he so skillfully frustrated Sherman’s advance on Atlanta. But after much back stabbing politics, President Davis relieved and replaced him with General Hood. Who immediately went out in front of Atlanta, attacked Sherman in a series of battles, and was soundly defeated for his efforts.
Hood in1864, IMO, totally destroyed the Confederate Army of Tennessee, when against all advice, stupidly attacked a much superior foe who was in very strong defensive positions at the Battle of Franklin TN.