Are you asking what is the difference in meaning between the two following sentences?
1)'By the time he had finished dinner, it was time for bed.
2) 'By the time he finished dinner, it had been time for bed'
There is a third possibility and that is to use the past perfect in both clauses.
3) By the time he had finished dinner, it had been time for bed.
There probably isn't much difference in meaning between any of them. If I was speaking about last night, I think I would use the first. But were I talking about something that happened a year ago, I think I would use the third.
I can't think of circumstances in which I would use the second. But this is a matter on which I feel very open to others' opinions.