using past perfect in a 'by the time' clause instead of simple past

How would using past perfect in a 'by the time' clause affect the meaning differently from using the common formula (past simple in the 'by the time clause' plus past perfect in the main clause). For example, what could the following mean?

By the time he had finished dinner, it was time for bed.

Solution 1:

The past perfect is used to talk about the order of events in the past. Your sentence means that in the past, he finished dinner and that when he finished dinner it was time for bed. Maybe it took him 3 hours to eat dinner and he finished at 11pm. The fist event is eating dinner, the second is bed time.

If you say "by the time he finished dinner it was time for bed," the idea of past order isn't really there as much.

The difference in meaning is minuscule. Using "by the time" just introduces another time phrase in the sentence. You could just as well say "when he..."