"Second transbay tube" and "increased capacity in core" together allow 24/7 BART service. This is a commonly requested thing, and these are the things needed to make it happen.
If BART had two tubes then they could run 24/7 and still complete the required maintenance with shut down periods staggered at different times for each tube. This would allow the full system to remain running 24/7.
There is more information about this on Quora: http://www.quora.com/Why-does-BART-need-to-do-nightly-mainte...
Having dual track throughout the system, and tube redundancy, allows track work to occur without delays and/or danger to track crews.