What safety precautions are taken for an airline prototype test flight?
The bail-out procedure is usually only available on the first and second prototypes, which are the riskiest because they are usually designated for testing aerodynamics, dynamics, performance and flight controls, as well as for envelope expansion. Obviously, it's only used as a last resort when recovery is deemed impossible.
In an efficient and professional flight test organization, each flight test is planned out in advance. The test requirements and procedures are written by engineers to ensure that they can be carried out successfully and safely, with clear pass/fail criteria, as well as abort criteria should airplane deviate from safety thresholds.
The crew, including pilots, flight test engineers, and ground telemetry engineers, are briefed on the test procedures and the applicable flight envelope and systems restrictions on the test day. Flight risks are identified and treated accordingly. For example, if a stall test is planned, the risk to spin/deep stall may be high enough to warrant the arming of the spin chute.
The restrictions are some of the most critical technical documents to ensure the safety of flight. They contain the following:

Limit the flight envelopes, and expand only insofar as the planned procedures can be carried out successfully;
Outline systems limitations and defects, and procedures to go with them;
Performance penalties, including takeoff/landing speeds/distances, that may be impacted by the non-conformant systems or failures;

Any non-remote failure or combination of failures would have been checked out in a pilot-in-the-loop simulator with the best-known flight dynamics and systems models/rigs. The results of the evaluation would be a major driver in adding/revising/confirming the restrictions and the Airplane Flight Manual under development.
Another layer of defense lies in the onboard flight test engineers, who will be monitoring the critical flight parameters relevant to the test. They direct the flow of the testing and have direct line of communication with the pilots. For critical flights, ground telemetry personnel will also be monitoring the parameters. Should the parameters fall outside the abort thresholds, immediate abandonment of the test procedure will be called and the pilots will initiate recovery.