I had my 600 mile service done shortly after buying. They did it while I waited, about 90 minutes. The manual section 6.2 says "the initial maintenance is vitally important and must not be neglected." It's reasonable to assume commissioning is needed and the warranty could be impacted. My dealer is top notch.
Now I'm going on 3 years and 8000 miles, having maintained nothing but the belt tension, tire pressure and brake fluid. While 4K service does not call for commissioning, 8K does. I'll take it in soon for 8K, and will also get new tires (same ones) and fork oil. The tires are great and have lasted unbelievably long.
I insist on no firmware upgrade. Everything is perfect. From my perspective, flashing it can only make things worse. How can I prevent accidental flashing? Can I make the EPROM read-only? Can I tape off the connector, or is the same connector needed for commissioning?