You have one of the best cross-breeds to be doing this with. I am taking my BCs on the Colorado Trail thru-hike next year, at least one and maybe both (one will be 7 and the other 9). Border collies and BC-crosses are definitely suited for the demands of a thru-hike, better than us I suspect. Your dog sounds like mine...calm when needed and boundless energy the rest of the time. Mine don't bark though and worked on cattle ranches with me for several years so I know how they are off-leash 100% of the time.
While the CT isn't the AT I can definitely report back to you on how things went with my dogs on a thru-hike. I am planning on slightly lower mileage days than most due to the dogs carrying packs and the extra water I will have to carry in some places. Water won't be as much of an issue on the AT I assume.
I have never noticed an issue with my dogs' paws due to the excessive hair they have for protection between the toes, but I expect that on a rockier trail it might be a concern. I don't foresee an issue on the Colorado Trail for us, but it might be something to look into for your pup with the rockiest aspects of the AT.
It took my dogs a couple of hikes to get used to the packs. My male bucked like a horse the first time he had to wear his with some weight, but got used to it very quickly. My female glared at me like I was killing her, but now she sees it and gets very excited because she knows what it means. Neither carries more than 4-5 days of food at the most.
I would love to go the FD route on the CT but the cost of the food is prohibitive for me. I will stick with their current dry food with lots of mail drops, or switch them to a high-calorie food such as they use for racing huskies/sled dogs.
If you want to read about my 7 day thru-hike of the Solitude Loop Trail with my dog(s), just to give you an idea, you can find it
here. I'm always happy to connect with other BC owners