The NT was my first long distance trip. I had the Hilleberg Nallo 2 person tent which is a non-freestanding tunnel tent. With all the possibilities of setting up my tent on convered concrete slabs etc (impossible with the Nallo), after completing the NT, I went out and bought a free standing tent for all my oncoming trips. Has been one of my best investments.
Biggest advantage of freestanding tents in my opinion - when setting up on a concrete slab or something similar indoor: Especially on the NT, you will have cool nights. The result is heavy condensation on the inside of the fly. This is particularly a big problem when setting up on grass/lawn. In the morning I would try to wipe down the moisture with my towel - but I was never able to get rid of all the water. I had to pack the moist tent and get going. During my lunch break I would take ou the tent and dry all parts in the sun. That would take only 5-10 min. But it is annoying to unpack and pack the tent 2 times a day just because of this. NOT unpacking and fully drying the tent will result in unpleasant smells and to me an "uncomfortable" tent each evening. So when camping somewhere I would always look for a covered place because I know it will save me a lot of time the oncoming day.
The above rarely occurs on the Transam: Here the temperatures are much higher during the night and you often never reach the dew point.