Well, it's kind of the same, but kind of not.
It really is injector duty cycle that determines fuel cut.
This is why on otherwise stock engines with just boost control, people living in Seatle, WA will hit FCO at 10 PSI (Very near sea level) and people in Calgary, AB can get to 14 PSI (~3800 ft altitude) with engines otherwise the same. The car in Calgary is getting more pressure, and more CFM, but the same MASS of air as the car at lower altitude, which means similar injector duty cycle. If that car is driven down to the coast without changing the boost controller, it will start hitting FCO a lot sooner.
The displacement of the Lexus engine isn't the issue, it's that the AFM body is larger, therefore it lies to the ECU, telling it that there's less air than there really is. The ECU then sets the duty cycle for the injectors based on that lower result, and gets more fuel than it expects. The result is that we get about the right amount of fuel, so the O2 sensor feedback tells the ECU that it's all fine (Assuming closed loop mode.)
Lots of people running pretty high boost numbers with the Lexus AFM / 550cc injectors, and making the kind of power that you'd expect.
I'm pretty sure that there is pretty good information on the MAFT Pro tuning with 550cc (Or indeed many other size) injectors. I was under the impression that what the MAFT Pro did (Among other things) was basically take the place of the AFM. It tells the stock system how much air would be coming in the AFM based on a different sensor, like a MAP sensor, so you aren't really changing engine management, or directly setting injector duty cycle. I believe that it also puts out a signal for the O2 sensor which can be tweaked based on a wideband, so you can tell the ECU to run a little bit lean in closed loop mode, in order to save fuel.
