I have found in most cases, the volume of tempo for soccer players at higher levels may actually impede speed development, mainly due to their current fitness level. As fitness improves, speed would improve with a high dose of tempo.
I have found this with a football player, who was improving steadily in sprint times, until an increased amount of running was added to handle their team workouts in the fall. Once this was added, times slowed down and we have had to since change his workouts accordingly.
100m involves speed endurance which isn’t specific to any sport except track. I have had soccer players who could get out for 30-50m but fade quick to those more trained in track specific events. The testing wouldn’t indicate much. The hand timed error shouldn’t matter as long as the timing method is consistent (same person etc) from pre test to post test.
Also, when you improve, you will know. My athletes have learned to feel things quite well, that when they don’t feel good during a run, they tell me immediately after. I look for technique and mechanics, then how the athletes feel and then stop watch, being the final decider on the rest of their workout.