bcm78:
Is there a way to disable those undervoltage lockouts in the Due?
No.
Converters have losses. Doubling output voltage more than doubles the required input current of that booster.
You stand a better chance by just connecting the generator to V-in (assuming voltages are within range of the Due). Maybe a fat capacitor (thousands of uF) can help bridge the startup current. Dunno.
Can't you use an Arduino that's less power-hungry?
8Mhz Arduinos can work from 1.8volt.
leo..