asking about the past perfect simple in this sentence

It's because the reported figure is a snapshot of a dynamic situation. Of that 12% only a small proportion will still be alive and they are now over 85 but we would expect the proportion of people over 65 to be higher now. Also the situation in 2000 is being compared to the situation in 1900 which pushes the discussion further into the past.

When talking about dynamic situations we often use the past perfect for quite recent events if, for instance, a police officer was giving a verbal report on a traffic situation he might say "We've been here ten minutes and the traffic had backed up a kilometre or two by then. We got them moving round the obstruction and things are nearly back to normal". The situation is dynamic because the length of the queue is changing while he's speaking but it is not two kilometres long any more.

Similarly in computing someone might say "The job started a minute ago, by the time I started monitoring it 10 000 records had been processed. There's only about 300 000 left to go now, it should be done in half an hour."