How do the to cards interact?

I understand that San San reduces the advancement requirement, but does it do anything for the effect on Project Beale? Or do you still only get extra points for tokens above 3?

It's the latter. You can score a Beale for 2 advancement, but to get an extra agenda point you still need 5.

The reason is because Beale says "for every 2 counters above 3", not "for every 2 counters above its advancement requirement" or something similar.

That is what I though, just wanted to make sure there was not some ruling that says something else. It is still good since it is a 3/2 agenda

Definitely. I think a textless 3/2 is worth playing; anything else is just gravy

Beale is excellent, and don't let the counter-synergy with SanSan put you off either. I dropped one in a SanSan server the other night and single-advanced, because I knew that barring any nasty surprises from the Runner, I could either lock him out with my Tollbooth and single-advance/score for two, or triple-advance and Astro-token for 3 points on my next turn. Alas he ran the Tollbooth so the rez cost left me having to score for single points, but still felt it was worth the attempt. In short, it's nice to have options