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 government uses pricing in a proposal to evaluate perceived value.  The CLIN pricing is what is binding once performance begins.  The key in your situation is that you have a CPAF contract arrangement.  That is why your CLINs ae set up with ceilings rather than specific dollars.  The government will pay all reasonable, allowable costs incurred by the contractor.  Its composite rate for a senior engineer from the proposal or even from Attachment 1 of the contract is not what we pay; we pay what the senior engineer that performed the task is being paid, whether it is more or less than a rate from a table(proposal or contract).  The pricing in the proposal gives us an estimate of what costs we can expect based on the forecasted rates and factors provided.