1. Eccentrics are used for tendinosis -- chronic degeneration -- because they create inflammation for the healing process.
For more details, wfs
(3 stages of "tendonitis" ... treatment differs depending on what stage you are at)
2. The problem with the stats is that you can't tell whether people were highly conditioned athletes or random joe blow.
You also don't know whether people are working through pain/tendonitis or not.
Runners are notorious for working through injuries to keep running... I wouldn't be surprised if those make up the majority of the running related achilles ruptures.
Properly structured S&C should theoretically prepare an athlete better for the rigors of the sport -- so yes, sprinting and running stairs can theoretically help. BUt too much can be too much regardless.
3. 40" is like the super upper limit of height depth drops are taken from and usually only by extremely well conditioned athletes (think people that have been training in their sport for 15-20+ years).
It's not just the 50 box jumps of 24" inches in workouts though. The former higher ones aren't done when fatigued. And they aren't coupled with other impact work in the same day/workout like you would get in a workout.
Don't get me wrong -- most of these injuries aren't sudden if the tissue is healthy. I would likely suspect if you look at the histology of the tendon even if there is no overt symptoms of indicator tendonopathy there would probably be some level of degeneration in the tendon from high rep overuse.
Remember, tendons and other connective tissues heal much slower than muscles. In CF you're constantly attacking the cardiovascular system and muscles with high intensity exercise. The things that will break first are going to be connective tissues like tendons (achilles, medial epicondylitis, patellar tendonopathy, biceps tendon, etc.), labrums (see SLAP lesion), possibly menisci with poor function,etc