I agree with Glenn’s view - the programme should represent both the contractual requirements as well as the realistic view of what is actually happening. I put put some notes within the narrative stating that it is acknowledged that this is out-of-sequence, but this is the risk th econtractor has taken on, and therefore has been reflected within the programme. The Project Manager can then accpet the programme (it is unreasonable to reject) but note that the accpetance recognises that the contractor has started out of sequence at their own risk.
It does seem odd that the contractor has taken on this risk, unless there are many discussions taking place giving them re-assurance that the acceptances are coming (with confidence).