I have been able to achieve less than 1/2" difference between two 1,000 foot measurements, when using a spring scale to maintain 10 lbs tension on the tape. I have had another person hold the other end, so there is less variance from placing nails and doing it all solo.
If you had a difference of two inches in two 1000-foot measurements, which is the more-accurate measurement? Split the difference, and maybe have the course short an inch? If so, the Jones is not precise enough to register the 1" difference. If you calibrate to 1/2 Jones click, then you may see a difference. That would magnify 5 times over the course of a mile, and 26 times over the course of every marathon measured using that cal course. 7" times 26 miles is 15 feet. That is a material difference, even though our SCPF is 38 feet.
I personally would rather have more precision in my calibration courses than in my race courses, since my race courses are based on my calibration course. I use an electronic counter, so I use 1/100 of a wheel rotation for my "clicks", which is more precision than a Jones will give. Therefore, that 1" makes a material difference in my measurements. I use the Jones for verification clicks, but the electronic is more precise. (That much precision is not needed, but since it is available at no extra effort, I don't mind using it.)