1) then why didn't they force them to use input from both? Why give this shitty design green light? Why outsource parts of the certification process to Boeing, the same company who's plane is to be certified?
Because of 2) obviously. All the money is gone. No budget for rigorous testing and validation of specs.
Outsourcing of certification predates homeland security - see e.g. mid-90s reporting on the 777 certification[1]. In fact, the idea of outsourcing parts of the certification process started IIRC in the mid-1940s. What did happen past 2001 (but not due to budget pressures) is that the airline manufacturers got the authority to appoint their own designees, and were allowed to self-certify.
Not for budget reasons, but for "deregulation is good" reasons. The money isn't gone. We've just got people who'd like "a government so small they can drown it in a bathtub". Well, it's drowning alright.
Because of 2) obviously. All the money is gone. No budget for rigorous testing and validation of specs.