BOAC - Good point engine thurst output is rarely identical.Even when I used to test new aircraft we had to set a specific N1 which meant the engine delivered the thrust it was certified to deliver, to meet the Production Flight Test Schedule, rather than its maximum...out of the crate figure.
I need to speak to the engineers though as I am fairly certain the FMC does not have this info. As far as I know there is no engine serial number/thrust info which has to be re-entered when there is an engine change. I can only assume the FMC driftdown altitude is based on a worst case thrust output for a generic engine.