"Since he did" vs "since he had done"

everyone! Could you please help me to choose between these two variants?

  1. "He said he had been working in this laboratory (lab) since he graduated."
  2. "He said he had been working in this laboratory (lab) since he had graduated."

The following passage in the section The disappearing past perfect (p51) from The Handbook of Good English by E. Johnson may help you answer your own question:

...more and more often, writers who are generally careful with their grammar do not bother with the past perfect when the time relationship is apparent from the context anyway.

Johnson notes that use of the past perfect when other words in the sentence (such as before or after) already 'express the time relationship' is regarded as 'redundant and therefore wrong' by some grammarians.

Johnson himself does not see redundancy as 'an ultimate evil that must be stamped out' but concludes:

...there is perhaps something slightly illogical about indicating time differences with both an adverb and a tense...Nevertheless, the past perfect is acceptable and to some ears preferable.

In your sentence 2 you do not need the second past perfect to disambiguate any 'time relationships', so it could be considered redundant.

For what it's worth I have a slight preference for sentence 1, but the choice is yours.