A good source is always the Official Guides. There is no question, at least not in 10th or 12th editions, in which a past perfect is wrong with the inclusion of such words. In fact you will not find many questions with the words before or after as part of the sentence.
However, proper usage of the Past Perfect, especially in written form certainly allows expressions such as: before, after, by the time, once, and since (among others). There is no reason why in the GMAT there would not be a use of a time expression or clue with the Past Perfect. This is not only wrong but also illogical. It is prevalent in other tenses (such as the present perfect, past simple, etc) and has indeed been used by the GMAT. See, for example, question 69 in the 12th edition which uses 'once' and in the example at the beginning of the chapter, the expression 'by the time' is used to denote the past perfect. If you can find counterexamples in the 11th edition, I would be more than happy to look at these.
So altogether, expressions such as 'after' or 'before' can be used with the past perfect (most if not all grammar books will show this to be otherwise), but at the same time it is certainly possible to use the past perfect without such expressions too when the context and sentence construction is obvious enough to warrant this.