I've got a YTS-82Z with a G1 neck and the intonation is definitely better than the neck that came with the YTS-23 that I traded in for it. Its intonation is also at least as good as (and mostly better than) the half dozen other saxes I tried when I bought it (Nov. '05)...
Intonation depends on right lengths, volume of the bore at various points, and such. It's not isolated just in the neck, but having an improper neck can screw up tuning for the reasons above (and more, i imagine)
I have a custom z alto which plays horribly out of tune. I believe the horn is fine and so is the mouthpiece so I think is the neck. On my tenor, which is also a custom z, the tuning isn't a problem. I have contacted yamaha and they said they will send me a M1 neck which apparently plays more in tune.