Yes you need the ECU flash via the Akro dealer code or purchase the ECU for the 1100 ,they run very lean stock and leaner with any slip on. I've dynoed mine already. And no one had been knocked back on warranty with the race ecu, that thread on AF1 has nothing official regarding this issue, nothing conclusive there at all.
Any Aprilia ECU used on your bike will be covered with warranty, a PCV or Bazzaz won't. I've been through all this with Aprilia Australia and these are the facts I've been given. I have this in an Email so that's good enough for me.
Street bikes are covered, If you're racing it, no it's not covered. No shock there.