Yeah, the way payout works is:
Base Payout + Negotiated Bonus + Secondary Objective Bonus / Extra kills Bonus + Repair Cost up to the negotiated compensation.
So if your mission is 65K + 250K Bonus and you have up to 400K in repairs negotiated, if you suffer 239K in damages, you'd get 65K + 250K + 239K. If you suffered 450K in damages you'd get 65K + 250K + 400K.
Repair has the potential of a greater payout if the mission goes bad. But if it goes great you may get a lot less than the negotiated bonus pay.
edit:
Also not that on the 2 or 3 mission operations, unused salvage and damage compensation carries over and stacks from operation to operation.