I did a quick google search and looked at the Oracle documentation for Flexcube. While I'm not 100% sure it is for the same version of software, the documentation appears to discuss this point.

  Overwrite default settlement instruction

  Select the ‘Overwrite default settlement instruction’ check box to confirm
  that the liquidation entries should be posted into the Internal GL account. 
  System posts the entries to the Internal GLs only if you check this check box.
  Otherwise, system posts the entries as per the settlement instructions specified
  for the component of the contract.

It seems to me that the docs say when the user doesn't check the overwrite default settlement instruction checkboxes, the software will xfer the money according to the settlement instructions. Either way, for approving almost $900,000,000 I'd take a second look before clicking the approval button on a subcontractor's work. Heck, I'd even check when approving this transaction for the VP down the hall.