FWIW, I just learned the the older ECUs (5am Magneti Marelli) can now be reprogrammed by some tune shops by purchasing a software key. Specifically, European Cycle Service has offered to do a full custom dyno-tune using the stock ECU.
Software key is being priced at $250. Dyno-tune is being priced at $600+
This seems similar to the ECU reflashing available, but with the added functionality of a customized map.
Here's the website. I'm having it done this weekend and will report back in early May when I get my bike back:
http://www.europeancycleservices.com/service/dyno-and-tuning/