Sentence Correction

The author is saying that "had occupied" is wrong because it is evident from context that Isaac occupied position far before Stephen did. Now lets imagine this:

1800: Jack is Dean HBS.
1990: James is Dean Busi. School at Harvard.
2010: John is Dean Busi. School at Harvard.
2015: Present: Stacey is Dean HBS.

And we say:

James occupied the same position at Cambridge that John occupied.

Above sentence is correct. And if we follow what author is saying then it mean that John occupied far before James which is incorrect. Also, it is possible that Stephen and Isaac occupied something at the same time, if not...how can we show that with different construction?

I am confused. I still think that "had" has to be there to show that Isaac came before Stephen.