well mercury uses pressure transducers in the cylinder heads to monitor cylinder pressure and to look for knock (which shows up very easily on the ocsilloscopes). Merc racing motors are generally calibrated to "lean best torque" meaning that for a given rpm, spark timing, throttle opening, etc, there is a minimum amount of fuel that is required to make power and not knock. That is generally where the motors are calibrated for. (note this for a simple EFI calibration). For an optimax motor, there is MUCH more complexity because there are many more variables... there is start of air, end of air, fuel air delay, fuel injection duration, spark timing, number of sparks (newer opti motors have multistrike coils that allow 2-16 sparks per cycle per cylinder). The current ECU's are much more complicated (with 3-d fuel curves, transient responses, warm up and idle maps) than the old school ones that are found on the original promax motors.
recalibrating the older ECU's on an EFI is simlar in principle to rejetting and tuning carbs, except with a computer, it is a lot simpler and it gives you more control (and you dont need a bunch of numbered drills!). Mercury calibrations are made to work on just about every boat, with any possible prop combination, under any condition (high to low altitudes) so sometimes the calibration is a compromise of performance and reliablity and functionality. By reprogramming or tweaking a calibration with a brucato PCU or similar device, you might be able to find some gains and make your motor run better under your conditions. Or, you might be more comfortable tuning closer to the "lean edge" especially if you are confident in your fuel supply. However, it is definately a "user beware" because if you screw up, you can turn your motor into a unusable pile of scrap aluminum very quickly.
Also, it is technically illegal to modify emissions controlled motors from something like 1998 and newer... so, user beware!
