In advanced auto tune, you have the option to set the Desired AFR. What does this setting do and when would one use it? How exactly does auto tuning the VE tables for a given desired AFR affect the map's AFR tables? Should it be set to match the target AFR in the cruise range of the map's AFR table? What is the relationship between the VE and AFR tables?

I also notice its default setting is 14.7. While this is stoich for pure gasoline, most parts of the US only have E10 available at the pump. Stoich for E10 fuel is about 14.13:1. Should the Desired AFR be set for that instead? Or should autotune be ran at the default 14.7:1 AFR, then adjust the AFR tables accordingly? Will the stock O2 sensors even work in the 14.13:1 range?

 

The O2 sensors have no idea what fuel you are running and do not care.
They only measure the O2 left in the exhaust.

It makes a difference what year and model you have.

Some of the older ECUs only ran closed loop when the AFR was set to 14.6.
If you have one of those, when you set the AFR to 14.6 and run E10 the O2 sensor feedback will automatically adjust the AFR to the Stoich value of about 14.1.

The newer ECU software allows closed loop in a "range" of AFRs, on Sportsters about 14.2 to 15 to 1 (E0 AFR, again E10 will adjust automatically in closed loop)

 

Sorry...should've specified. It's a 2017 Fatboy.

 

That year and model is lambda based and should allow closed loop in a range of AFRs between about 14.2 and 15.0.
Choose a value in that range, I would accept the default from the FP3 and run auto tune.