I think you have to look at this as energy transfer.
With no gate pulse, you are right, there is no conduction below main bridge cut in.
If you gate the mosfet you store energy in the inductor. When you turn the fet off the energy has to go somewhere. There will be a large voltage spike and during the interval when this spike is above battery volts current will flow into the battery.
With small fet conduction angles, the energy will be small and only a momentary current spike will flow. With about 50% fet drive pwm the energy stored will be such that with a 2;1 boost the thing behaves more or less as a stiff 2;1 voltage converter and energy will be transfered during the whole of the fet off period.
The thing will still boost some energy from considerably lower than half battery volts but conduction will be for a shorter period than the fet off period.
The prop is also an energy source. If the pwm is too short the prop will have to run fast to deliver its energy to the battery. If the pwm is too long the prop will run slow.
The maximum energy is transfered when the prop runs at a speed that keeps it on the peak of its power curve for that wind speed.
The system is stable at any point, the available energy from the prop will be transfered. The prop speed will settle to a point where its available energy is transfered. It is the same as a current limited circuit, power flow will sort itself out and the supply voltage will adjust to suit.
Even if the voltage converter had a precisely defined ratio it would still be stable because of the series characteristic of the prop's power capability.
You must limit the gate drive, it must never go to 100% ( limit it to 60% should do)
At 50% the alternator - converter combination will be too stiff and the prop will stall just beyond cut in.
The analog control works by feeding back a current signal that phases back the pwm.
A high gain loop would result in constant current output and the prop would run away.
As you lower the gain the current rises, the lower the gain the higher it rises until at zero gain you are back at fixed pulse width and stall.
By choosing a suitable gain you let the prop speed rise at a rate close to that needed to track maximum power.
I have no idea how you do this by digital means, you may be able to implement a variable gain or you may have to attack things from a completely different direction but the end result must be the same. You need a pwm for each wind speed, chosen to keep the prop output a maximum at that wind speed.
Flux