As someone who just recently graduated out of BCT, I personally am appreciative of the calcium bar being provided to myself and my fellow recruits. Our "bar time" was a bit of an end-of-day ritual that my platoon used to relax a little with one another and our DSes occasionally used it as time for AARs. Some of my Drill Sergeants were new, so they used the bar time to get information out of us about our training, what we thought could be improved on, and generally just to make sure we were learning what we needed to. If we missed something or misinterpreted information, they used the bar time to correct us or made a note for the next day. It helped some people a lot.
The bar also helped myself with PT tests, as I never went to sleep or woke up hungry and could perform better the following morning. It wasn't a big protein bar or anything like that, and I doubt it had as much nutritional value as I think it did, but it was a mental tool I used.
Whether it helped with stress fractures and what not, I'm not a professional but I can say that only two people out of my platoon of 70 went to the Physical Trainer for them during the entire cycle. Everyone else had strained muscles or something along those lines. Other platoons had similar numbers. We had very few people on crutches or missing training events throughout the cycle.
The best part was when we started finding the things in MREs. We weren't supposed to eat more than one in 24hours apparently but we'd end up getting them in the brown happy meals for lunch or something the next day.
Chocolate is the best flavor. Apple-Cinnamon? Not so much.