If, in 1999, you opened a copy of Scientific American in August 1999, you might find an article that saiid something like
A planet called HD 209458 has been discovered.
Present perfect is used rather than past simple because discovery has a lasting effect: once discovered, a planet generally stays discovered.
The speaker in this video is reporting what happened in 1999: he can't just use present perfect, otherwise it would sound like it just happened, so he backshifts and uses past perfect.
That all changed in 1999. A planet called HD 209458 had been discovered.
Using simple past in the sentence as it stands does not sound right, because it is missing a crucial piece of information: when it happened.
A planet called HD 209458 was discovered on a very short orbit around its star.
This could be rectified by merging the two sentences, so that the date is directly associated with the simple past:
That all changed in 1999, when a planet called HD 209458 was discovered on a very short orbit around its star.