Don't know what Mr. Manahan would say but:
1. HART, not the City Council, writes the contracts to include cost-containment measures.
2. (a) HART has changed from design, bid, build contracts to less costly design-build contracts for the last half of the project, (b) reducing unnecessary features in stations in the Airport Guideway and Stations segment, (c) expediting the pre-construction design work, such as utility location and geotechnical analysis to reduce time in heavy construction.
3. There are numerous affordable housing projects proposed, but you don't get firm commitments until it's certain the entire system will be built.
4. Affordable is the goal, not low-income. Affordable (80-120 area median income requirements) are different from low-income, like Section 8. 
5. The question is not only hypothetical, but also contains the assumption that costs will increase, even though the latest contact for the airport segment was below budget.