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

The terms "Build to Print" and "Build to Spec" are not FAR or DFARS terms; we did find "Build to Print" in appendices of the NMCARS.  We cannot comment on the pros and cons between the two approaches.  We are not clear why a company building to a specification (presumably a specification we agreed with or gave to the contractor) has a greater chance of losing configuration management than when doing a "Build to Print".  More to the point, if Commercial Off-the-Shelf (COTS) items become obsolete and need to be replaced in a follow-on contract the Government would generally be responsible to pay for updated COTS items.