Context is everything, resistance is futile:
That little word so indicates something happened before the two things mentioned in the sentence:
The afternoon had been very hard as many candidates showed up.
So, before the young man had had a chance to say anything John had given him an application form.
The candidate spoke for five minutes without stopping. So, before the young man had had a chance to say anything John had given him an application form.
Without knowing what precedes the "so", I would eschew calling it in favor of the simple past. The answer is that it depends on the broader context. A broader context, called a co-text by some linguists.
One can easily imagine that the two activities with the past perfect precede the action in the simple past of the first sentence. Why not? It's perfectly possible.
Naturally, in another context, one can also write:
The young man was late and before he had a chance to say anything John had given him an application form.
The takeaway is this: context can come in a preceding sentence and is not always at the level of a single sentence.