The 6000 point thing was an arbitrary goal created to address someone's contribution to the site and their dedication. Pokebase is the easiest to get points on and therefore it became the section that you needed to have points on. It was also the most active section, so knowing what you're doing and saying in the green was arguably more important than the orange and grey.
As to why Pokebase only - a couple of reasons.
It was just easier having a single goal rather than various possible goals. PB is the most active section anyway and the easiest to get points in as mentioned, so virtually everyone would get 6000 there before 2000 and 1000 in Meta and RMT respectively (it is 2000 points to edit in Meta btw, I know because I am only one of two users to ever be able to edit in Meta before Pokebase).
Actually, thats relevant too. Only 2 users have reached 2000 on Meta before they were Expert - me and Ayan. Likewise only 2 users have done the same on RMT - JCM and SlipperyDevil (the latter of which only hit 1000 after he left the site so really only 1).
The point I'm making is that it was never an issue. It didn't happen because it never needed to happen.
Also Mods can just promote at will now so it's not relevant anymore regardless.