This is how I see it. I might be wrong and my theory might be a bit silly or don't fit completely, but this is how I explain it to myself. The Pluto we saw in the future, during the Black Moon Arc is the original Sailor Pluto. As she was guarding the Space Time Door she didn't die like the rest of them during the Silver Millenium, so she had never be reborn. Once her original form died, as a Sailor Senshi her soul was reborn. Neo Queen Serenity made it so her soul to be revived in Setsuna Meioh who might have been the destined human vessel, which has never awakened till needed. As she was needed in the present she awakened and got her memories back, but in a human body.
Another possible explanation is she exists in every time period as she exists beyond time, so there is a Sailor Pluto in every era.
Season 2 Pluto either has never met Sailor Moon or is pretending to have never met Sailor Moon (the latter being unlikely). She has always guarded the space-time door. Therefore my current belief is that she is the original (pre-Earth reincarnation) Pluto. No more bound to the 30th seki than any other time (except that she chooses to exit her post and die there). When she dies at the end of S2 she is later reincarnated on Earth as Setsuna. So, it is in my belief technically possible that re-incarnated Setsuna could meet her original form through the space-time door in 30th seki Crystal Tokyo palace. I don't claim to be right, just sharing my thoughts. I do not believe there are multiple parallel timelines in Sailor Moon.
The Sailor Pluto in the Black Moon Arc is the Sailor Pluto who stood at the Time Door and was also the same Pluto who was summoned when Saturn was awakened. When she died, NQS originally had given her a place in the castle to rest in peace but once we get to the third arc Naoko Takeuchi wanted to revive her and thus she allowed Pluto to be revived as Setsuna.
Setsuna may or may not have lived from natural birth which is up to people's interpretation.
Which brings to the next point.
Sailor Moon StarS Arc Manga Spoiler
="As Eternal Sailor Pluto appears in the 90's, there's a Super Sailor Pluto that appears in the future 30th century. Chibi-Usa may have meddled with it but what happened in this future Pluto's life. Possibly the future incarnation of Setsuna who resumes her duties at the Gate? Could she be living and connecting with her past self so Setsuna's knowledge of her life is beyond space and time?