How?um, if you play VLR first, you will ruin the story of 999. And if you're ruining the story of a VN, you're kind of ruining the experience.
Does VLR
tell you who was in the coffin before door 9 and in the safe
tell you about the relationships of the characters
When you play VLR for the first time
it's probably like finding out about the whole "two different places with psychic power training" for the first time anyway. In a way 999 probably kinda wrecks any major over-arching plot things that will happen anyway since you go "oh it's probably just that happening again" and it becomes more about the characters