I was wondering if you could add the November 2009 beta version of VVVVVV on here as a category extension or something, or if is not really worth to add it at all.

I don't really see a good reason for that to be a category for a couple of reasons.

1. Is there a publicly available download link? I couldn't find anywhere to download the beta version officially. If there's no way to distribute the game, the leaderboard will be inherently unfair because not everyone can compete.
2. What does it add to the leaderboards that isn't already there? I think it's in a similar position as Player Level speedruns, where it wouldn't be a very popular category, since it's not necessarily the most polished experience you can have with the game. The official release has been patched many times with good reason.
3. Where would you draw the line if someone asked about adding a v1.0 category? A v1.2 category? Adding version exclusive leaderboards is risky, because it unnecessarily divides very similar categories for no reason.

If we were to create a VVVVVV category extensions page, we would certainly consider it IF there were a publicly available download link, but other than that I don't think adding a beta leaderboard is worthwhile.

As a side note: The current Any% WR may only be achievable on v2.0, but you would still be allowed to submit an Any% run on any other version. There is also a publicly available download of v2.0 on Steam.

Makes sense. also It seems that the beta was leaked so it was never originally intended to be released. http://distractionware.com/blog/2009/12/final-push/