A good Bachelors degree will prepare a good student for replicating science, and a good Masters degree will definitely leave a motivated and skilled student with a good advisor a master of his or her specific field.

The problem is that grade inflation means the majority of students will fall short of these goalposts. I agree with your assessment that undergrad degrees represent hurdles, regardless of whether a student is planning to stay in academia or not.

My experience with getting a Masters degree was that it was really tough work that required my full dedication for two years. But I had a world-class scientist as an advisor breathing down my neck the whole time and expecting results, and my experience doesn't seem to match that of many other MScs I know. Some departments seem to be "degree factories"; it takes an unreasonable amount of effort to follow up students in the classical "apprenticeship" tradition described by GP. It would be very strange if every department at every university managed this level of dedication, with student numbers being what they are.