The answer is actually reasonably simple: US Civil War armies sucked at identifying bodies.

At the time, the idea of wearing identifying markers such as dog tags was not a necessarily new or radical idea, but it wasn't one that was implemented on any large scale. Before battle, it was common for soldiers to take off their heavy packs (which might have personal effects useful in identifying individuals) and leave them in a large pile someplace to come back to later, assuming anyone survived. If a unit made a hasty retreat or routed off the battlefield entirely, it was not uncommon to just grab the nearest pack and make a dash for it, personal effects be damned. Your pack had food, a tent half, a blanket, and that's all you really cared about. If, after the battle, packs were discovered containing the personal effects of someone who, as you said, was missing from the roll, he might conceiveably be listed as "missing."

It also must be remembered that the primary way of recognizing corpses would be asking people who knew the man who he was alive. Battlefield looting not leave a man with no personal effects at all, and unless he had his name sewn into his uniform, all you might know about him is his corps, division, and possibly regiment if they had a distinctive uniform. You might not even be able to tell which army he fought for, in some cases! To even further complicate the matter, (primarily civilian) burial parties might take several days to reach the area of the battlefield in which any particular soldier fell. Decomposition was not a kind mistress; you might know a man for years, but put him out in the hot sun for 48 hours, and he might be anyone. The Union Army had no dedicated infrastructure beyond ad hoc burial parties to inter the dead, so it was often up to the citizenry of whatever nearby town to bury the dead so as to avoid the overwhelming stench and possible outbreak of disease. Unless a Union soldier had identifying labels, he was buried by his friends, or he died in a hospital after giving an orderly his name, he might be buried as an unidentified soldier, and listed as missing from his unit's muster.

The Confederates had it worse, arguably. At Gettysburg in particular, there had been no large scale efforts to bury the dead of July 1st-3rd. Many of the areas captured by the Confederate Army were not retaken until the 5th, and by then the elements had truly taken their toll. They were buried unceremoniously in mass graves, quickly and sometimes rather carelessly, so as to avoid the overwhelming stench of decomposition.

Another not inconsiderable factor in the large number of missing might be desertion. The vast majority of soldiers fighting in the war were hastily trained citizens and militia, not noted for their rigorous discipline and dedication to the army life. Especially towards the end of yhe war, there were even men conscripted into service. Fighting and dying might not be especially high on their list of priorities, so they might take any chance provided to sneak away from their units. Perhaps under the guise of helping a wounded friend to the rear for medical attention. Perhaps pretending to be on a message running assignment. If these men were nowhere to be found after the battle but were not found among the the dead, they might be listed as missing.

Lastly, being captured would typically get you listed as missing. This doesn't especially need any further explanation. The idea of carefully listing every prisoner and sending a list out of who exactly you had captured was not very high on anybody's priority list. POW's were more often than not herded into large camps and left there to fend for themselves until a prisoner exchange could be arranged. If you weren't among the dead, and nobody had seen you get captured, you were listed as missing.

I could not speak to the specific examples of Union soldiers in static positions at Gettysburg, but I can only imagine you are referring to units on Culp's Hill. Very few other positions were continuously manned by the Union Army over the three days of the battle. This might be explained by a combination of desertion, poor record keeping, and the dead falling where they might not be discovered. Culp's Hill at the time was very heavily wooded and stony, so any number of bodies might be hidden in narrow rock formations or in heavy underbrush. That being said, yes; it is entirely feasible that a body might be so badly damaged by artillery or other battle damage that there would be simply no hope of identifying his corpse, meaning he would be listed as missing.

And, finally, to the last point I wish to cover; the the "missing" on Civil War casualty lists has the same basic meaning as today. With the advent of formal identifying markers and (perhaps even more influentially) DNA testing, the possibility of any given body that can be recovered going unidentified is very unlikely. It is only those who fall in jungles, on mountains, in the sea, and in other inaccessible locations, or who are captured by enemies not willing or interested in declaring that they have captured a soldier that are listed as missing in this day and age.

A good resource would be the Gettysburg Compiler at

https://gettysburgcompiler.org/

Another interesting collection of primary sources I've recently discovered is a collection put together by the College & Resource Libraries which can be found at

https://crln.acrl.org/index.php/crlnews/article/view/9314/10416

I hope I answered your question!