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

Firstly, I didn't know that what I've always called "pluperfect" is now usually called "past perfect", so thank you for highlighting that for me.

My understanding of the question is that you are examining the difference between these two sentences:

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

I would say that there is very little difference between the two. I would infer a little more finality from the first one, in that dinner was definitely over and done with, and that he had left the table. The second would suggest to me that he had just finished eating. Hence, I would say that the past perfect version implies more completeness to the activity than the second. But as I said, the difference feels minuscule to me.

It's an interesting question though and, like WS2, I'd be interested to read other people's take on this.

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..."