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Why should it be too late? You increase bone density by training. If the military finds people have not enough bone density they need to add more fitness exercises (e.g. strength training) to initial training.

What young, obese people are suffering from permanently decreased bone-density? If anything their bones should be strong from moving around the extra weight all the time. These are young people, they should be able to adapt if given enough time.

What are you on about? It's well known that bone density and strength increases with load: https://en.wikipedia.org/wiki/Mechanostat

If you didn't learn this in grade school it might already be too late.