I have/had both 2005 ZX10R and now have a 2009 ZX10R in a race car not a bike so take that into account.
When I got the 05 I did some basic digging about TRE and different maps for different gears. At the time the best knowledge claimed that 5th gear was the least restrictive in terms of making HP/TQ. To test this I built a resister network that plugged into the harness and sent it to an engine builder friend and asked him to make dyno runs on one of his engines with a stock ecu and see if he could find the "best gear"; the results were inconclusive and eventually I used a resistor for 5th gear. My on track data acquisition system (fairly sophisticated system) could not see a difference in acceleration at ThunderHill, CA between the ecu in 5th full time or just giving it the actual gear signal.
Now fast forward, I have a Woolich Log Box Pro and have looked at the ECU maps for both the 05 and 09. What I note is for the 05 the ignition map editor has no pull down for gear setting. What I have also learned is if the gear position indicator fails the fault value for gear is neutral.
On the 09 the the ignition map editor has no pull down for gear and the gear position sensor fail mode defaults to 6th gear. The only thing I see of interest to me is the top speed limiter which limits the RPM in 6th gear. The only maps that seem to have gear pull down menus are the STP and the fuel trim, and the differences in the maps are small. I'm still thinking about neutral vs 6th gear.
I have only run the 09 once with marginal results, mostly due to me. The upper injectors were not all working at first most likely due to the engine sitting for an extended time. It has 4200 miles on it but I have no idea how long it sat in the salvage yard in Florida before it came to me and salt air is not great on injectors. There were other issues that are mostly the unintended consequences of changing engine platforms.