Regarding if statements 2 and 3 are contradictory to one another: statement 2 is "softer". The use of the word "likely" allows for some flexibility. Statement 3, in contrast, is much stronger: "it is NOT POSSIBLE to predict..." Combining the two statements, we can say that, while it isn't possible to predict entire body bone phenotypic changes, it is likely that those changes are age-dependent.
We have evidence from the passage that those changes might be age-dependent. From the first paragraph: "After it is formed, adult bone is continuously remodeled through the activity of osteoblasts and osteoclasts." This brings us to your last question: whether or not age-dependence is a phenotype. In the case of statement 2 in question 122, the phenotype in question is the deviation from the wild-type phenotype. That deviation is likely to be age-dependent. In this passage, age is a factor that contributes to phenotype change, it is not a phenotype on its own.
Hope that helps.