There's a really interesting article in May's Sport Rider where they tested a stock ECU modified by ECUnleashed ($449.00), along with a PCV as well as the Autotune, on one of their long term test bikes, a (now) Graves piped YZF-R1. ECUnleashed currently cracks the Hitachi ECU's (and Renasus CPU's) on Yamaha's, and they note similar ones are found in some Kaw's/Suz's. They can actually remove all the potting compounds to access the circuitry and spend a lot of quality time back engineering and modifying these ECU's.
They don't mention the SKRR yet fwiw, and interestingly they consider the Honda ECU made by Keihin a "throwaway" as there is no easy way to access the internals (probably not a good sign for us

).
Once cracked they can change a myriad of settings within the stock ECU (rev limiter, fueling at closed throttle, add quickshifter controls, etc.). On one of their personal bikes they have even managed to add an electronic cruise control simply via reprogramming. As I read the article, from a strictly HP/TQ/Rideability standpoint the PCV and AT will deliver comparable results, with the advantage that you don't need to send your ECU for reflashing every time a fueling change is warranted.
It appears that in the not too distant future this will be a very common mod as these types of companies catch up to the car guys, who are a few years ahead.
This probably doesn't really answer your questions, but is a very interesting article nonetheless and well worth the read.
Edit: FWIW I did send them an email asking if their working on the SKRR.