bit more time to type so will try and expand..
the Apexi is a nice unit.. you get the commander which has various uses for monitoring or even altering certain things if needed etc.. this also has disadvantages if someone alters it for the owner, by accident etc..
The board within the original ecu retains the knock control.. which means say you get a bad batch of fuel it will retard the ignition and save the engine../ with the apexi the engine light with flash and it is down to you to back off to save the engine.. with the apexi you know you have a bad batch of fuel.. you can drive gentle and refuel or add booster.. with the board you don't know it has retarded the ignition removing power.. both suit different view points etc..
the overall result is the same.. ie. there is no real reason one should end up with a quicker car with one over the other and the car should drive in the same way etc they are both a means to the same end.. the Apexi has been around longer and therefore the alterations such as z32 maf sensor and other alterations which relate directly to the ecu are more common and therefore solutions established.. if the car is going to be modded a lot (bigger cc, 400+bhp, etc) then currently the Apexi is easier to map.. but that is a short term situation.. The Apexi is still very well known and a lot of people buy the Apexi PowerFC and then get it mapped as it is a well established route and a lot of people have done that before asking me to map their car and therefore the ecu board is not discussed.
Simon