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The throttle body does nothing with regard to fuel cut.

Swapping out the AFM for the Lex AFM shifts how much air the ECU THINKS is entering the engine because it lets in more unmetered air. So the ECU still sees a pattern which reflects 50kPa with the normal housing, but there's air sneaking in the back door and the engine is really getting 65kPa.

The thing about the IC letting you run more boost is rather simple.... Well, I'll try to simplify it and keep it accurate enough. There is a pressure drop across the IC. An inefficient IC may see a 5psi drop. This means that while your turbo is cranking out 15psi your intake manifold and engine are only seeing 10psi. By putting in a more efficient IC (with only a drop of 2psi) your intake manifold will see 13psi instead of the lowly 10psi. The turbo is still cranking out 15psi. The air is just having an easier time reaching the engine and is considerably cooler now too. But the volume of air moved at any period of time shifts too though and as such your fuel cut doesn't shift too much. Long story short: Fuel cut is determined by the measurements taken on the turbo side of the IC whereas what the engine sees and what you see on the gauge is determined at the intake plenum.