Hmm looks like someone put that 2 on the wrong side of some parenthesis: (1/3)*2=2/3, (1/3*2)=1/6.
I believe the bonus should be:
Bonus from buildings etc. 1/3 free 2/3 just plain increase that you have to pay for
Bonus from starbases, and resources: 2/3 free and 1/3 paid for.