GMAT Sentence Correction (SC) | Re: Some of the most significant buildings of the early Scottish Celtic

I picked the right answer but I have two problems.

1) Do we always need to use the past perfect (referring to the past) along with "by the time" ? Is the past perfect use incorrect ?
2) I am not English and I am not sure of the meaning of "some of the most significant buildings of the early Scottish Celtic period had long since been destroyed". Does it mean that those buildings were destroyed centuries before the end of the Middle Ages ?

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