At what point in the rankings is having a PhD from one university no different than a PhD from another (differently ranked) university?
It's worth keeping in mind that the overall university ranking is not synonymous with how they are regarded in the field.  Even the breakdowns by discipline are not always going to reflect how the university is perceived in a specific field.  

For example, a university may not be in the top 10 in these overall rankings or even in a discipline (e.g., Computer Science), but they may be considered in the top 10 or even the top 5 for specific research fields (e.g., Database research).  

For a PhD, the ranking in the field will probably carry more weight than the general ranking of the university (depending on the field), as will the overall quality of the research.