The ECM will need to be played with and a performance free flowing air filter added to get the best from a aftermarket exhaust, however some gains are realised without it, but some problems are also created!!
To be perfectly honest the standard ECM's work ok with the standard set up, but have plenty of untapped potential to be made better by someone who understands how to tune these bikes. They come running from the factory to meet the required government pollution laws within the countries, or even states that they are delivered to for sale.
They are definetly not optimised for maximum performance but rather for required government regulations.