I am nowhere near the expert on this as is freak from KFFL, but I remember something about 100m times containing 10-yard splits, the first four of which were used (largely) as the basis for the 40 time extrapolation.
I have it in my head that the combine utilizes electronic clock stoppage (triggered by the runner hitting a string), but that starts are still hand timed. Pro days are even more informal, as I believe everything is hand-timed. I'm not sure of this, but I think it's the case.
Don't get me wrong - come draft time, I live and die with each 40 time the media reports. But it is quite interesting to explore the validity of it all, and see that these times that are so oft-cited stand upon the flimsiest of foundations.