had done

[Taka]

She felt disappointed to find that she hadn't done anything, compared to what those geniuses, such as Newton and Einstein, had done.

Does the part in bold have to be the past perfect?

[Tdol]

I think you could also use the past, but I would use the past perfect.

[Taka]

So when you native speakers see 'past→past perfect(a)→past perfect(b)' in a single sentence, you take (b) as the past still further back than (a)?

[5jj]

Not necessarily, We use our previous knowledge, and knowledge of the full context to decide what happened when.

[Taka]

Then why do you think the past perfect is much preferred as to the last part of the sentence in question?

[5jj]

Nobody said it was 'much preferred'. Tdol would use it; I would too. The sentence allready contains a (necessary) past perfect, and, as the achievements of Einstein and Newton were some time before those of the subject of the sentence, I think that the past perfect is more appropriate.

However, unless you happen not to know who Newton and Einstein are, then the sequence is fairly clear, and some people would use the past simple for the final verb.