I used to work for British Aircraft Corporation building BAC 1-11s. The standard tolerance on parts was + or - 0.010" (10 thou.) In theory if you added all the tolerances of fuselage skins together you might end up with a variation in length of about 0.2", (fuselage about 100ft long) but since the sections were joined in a jig I doubt there was much difference in overall length.
I don't think Boeing do things much differently, so to get an error of 3 ins seems unlikely.
I guess the B787 might be built a little differently.
Holes are often pilot drilled in skins and left blank in the ribs and stringers to enable adjustments to be made to the fit before final drilling and riveting.
Some clever person at Edgely tried to final drill all parts for the Optica before assembly. CNC accuracy? I believe the fitters had to do a lot of fiddling to get the thing assembled. Then they went bust.