Good that things are improving for you, some strange things can be seen in litters of pups, but it is usually dietary, when it's the joints that are affected like that, and don't forget also that the 'lumps' that can be seen on the front legs are growth plates, that start to flatten out to the same size of the rest of the leg once full size has been attained.
In regards to big breed, yes well that is true in a way, they are a big strong dog in a medium size package and they grow quite quickly, too much exercise too early can cause damage.
I like to keep the weight off my pups, prefering to have them a bit on the lean size, until about 9 months old, then I GRADUALLY start to feed them up. By the time they are mature, I have a dog of the right build and weight.
Be careful with overcalcification it can happen. Stick to the recommended dosage, and don't be thinking more is going to be better! It doesn't work that way.
I bred them for 20+ years. So I should have some idea!
Hope you have many years of happiness with your new puppy.