Lets--
A good way to start might be a 3-point stance. Better than a standing start, and more forgiving than blocks. Actual position can be adjusted to suit your taste.
Without electronic/optical/optoelectronic timing devices, measuring flying-start stuff accurately is essentially impossible.
If it's done over a longer distance you won't have anywhere near an accurate read at either the exact start, finish, or both, depending on your position.
If it's done over a shorter distance at higher speed, there is more room for error due to the increased difficulty in judging position at higher speed.
Electronic tools can help, but must be set up and used correctly. More than being accurate, they can be repeatable if used consistently, and if baselines are developed.
Disclaimer for the rest of this post: I know nothing about distance training or distance race strategy training.
If it were me measuring distance runners doing 100's, first of all there is no way I would do it from zero velocity. Totally irrelevant to distance racing. So, I would do it at speed.
I would probably simulate race conditions somewhat. I would have them run 100m or 200m at what they consider fast race speed; have them run by an automatic start with maybe 120m or 130m to go, and tell them not to start "sprinting" until there is only 100m left.
I would then set up one end timer at the finish, and another maybe another 20m-30m down the track.
I would take as a measurement the time for the first 120-130m, which would include 20-30m of their fast race speed--which should be consistent, so it would be the same in all of the measurements and wouldn't matter. Those first 20-30m would be used to ensure that acceleration from the very first instant the sprint is started is captured.
What I would actually do would be to time segments over 400m. I would have them accelerate to fast race speed for, say, 20m before crossing the start line, and run varying profiles around 400m, and set up timers at various locations of interest. I think that the possible profiles of the last 400 of these races is of much more interest than, say, a flying 100 capability.
But again, I know nothing about this sort of distance training.