Well, that is a very GOOD question. I will attempt to give you *my* answer, but, it will be different from other thnough hikers' answers.
First off, through hikes are generally done solo. Even if you start with a partner, this doesn't seem to last. A gentleman friend and I did the NPT last year, for example. A shorter through hike of about two weeks. We met up at Blue Mountan Lake (Lake Durrant Campground where we spent a few nights, I changed back to my hiking boots, grabbed the saw - the wife dropped them off - took a shower, et al, as he waited for his resupply box from Vermont) and we sort of followed each other the rest of the trip.
Typically he would take off first every day. Sometimes by an hour or two while I went through and cleaned up the campsite, burned what trash I could find, packed bits of aluminum foil/plastic/tin from the area, cleaning up, generally. I really hate a dirty campsite. I seemed to hike faster than he did, so I would catch up 2-3 in the afternoon and continue on to the next camp site. Not that we avoided each other, we had different priorities. We covered the same ground at the same rate at the end, more or less. But, we didn't hike together, much. The trails were not that bad. Companionship, was more important to me...just knowing that someone was out there within a few miles made it easy. Solo hiking can be bad for the lack of it. This is one aspect of through hiking that is different from other types of hiking.
Supplies are another. I can pack enough for a couple or three weeks. Once things start to run out, I have to pick things up as I go. I hate schedules. As the above shows, waiting for a supply box over a weekend (Saturday/Sunday) or arriving too early and missing it, makes life rather difficult. I don't. I hike at the pace I hike. When I get to a convenient stop, I will resupply. Often, this means purchasing things I don't normally carry. Eggs for instance. I am always looking for protien. Eggs are heavy, and don't keep all that well. But in the middle of a through hike, I will often get a dozen. Hiking a few hours to camp is not a big deal, by then. I have a few, with spices, foraged greens of some sort, even green apple bits, makes a good supper. Mornings the same, with boiled eggs for lunch and the next supper. Guess what. I was sick of eggs at breakfast. That box of Bisquik is way too big to consider carrying. I fill a baggie or two, and dump the rest. Rice/pasta sides are a staple, but they might only have one or two types. Difficlt for the next week or two to eat the same food, left, right, left right...you get sick of them. Fuel is usually sold by the quart. I carry 12oz...a waste, I don't have room for more. The little Murmur is a tiny pack. I hate to waste stuff, not good for the environment, nor *my* wallet. Difficult at best. But, interesting, none the less.
Walking on a mountain ledge can be dangerous. I don't really mind, but, I think my wife might not want me to fall. Maybe, I will take a safer route...Not about me, so much as others. But, keeping myself safe is often an important consideration.
Camping for a week or so in the back country will put you at ease with your surroundings. Ooops, forgot to hang the bloody bear bag as my eyes snap open at midnight. Ahh well, it will make a good pillow... Not safe but better than nothing.
Discipline goes...washing every evening is a chore. At least wiping down your body with a wet bandana. An easy thing to let go for a couple days...till you smell yourself after 6-7 days of letting it go.
Working like a dog up the hill...only to find you have to go DOWN the bloody thing on the Other Side...hey, ha. At least you found out what was there.
And the trail. Day after day of slogging, walking, climbing (up or down) sometimes crawling. You start wishing someone would pave the bloody place. Till you hear the peepers at night. Nice sound...at 2100, not so nice at 0100. Frogs too.
Then there is that immense sense of satisfation at the half way point. Yup, on the downside. Lots more work ahead, but a good feeling. The night before completion is restless. Despite knowing it is just another night. I will finish tomorrow. Rain, lightning, blizzard conditions...well, I've seen worse. You have hiked through stuff as bad. Come hell and high water, I will finish tomorrow. But, that is tomorrow, get some sleep you dummy! Hmm...leftover supper was great. "Hoarded stew" I think it's name is. All the little bits of dried beef, jerkey, salami, flour, 1/4 packets of this and that, and a dollop of "gotta eat that". . . a BIG meal and tasty too, nope it no longer matters what's in it as you found out last month when the store you had planed to resupply at was closed when you got there, forcing you to stretch 3 days of food for a week. At least the gas station was open and you got fuel and *some* chips.
Other than a few minor things, you are correct, just another hike, 'cept a little longer.