This response is based on the information provided.  We suggest you discuss with your contracting team, program manager and/or legal department as appropriate. 

You have the ability to structure you contract in a manner that makes the most business sense within the rules of the AR/DFARS/AFFARS.  The best way to accomplish the contractor's request and ensure the government's interests are protected would be to have option CLINs for each phase and a matching bond CLIN of the appropriate value for each phase.  When exercising the first phase you would also exercise the bond option for that phase.  If the work is not progressing as planned, neither the task nor the bond CLIN need be exercised until the previous wok is satisfactory.

The risk you run is that the bond may not be available at the time of exercise.