The ECU will be fine with the MBC - it will have no clue about it. Keep in mind that even though the MBC is tuned all the way down your turbo will still be able to boost to whatever your wastegate spring is calibrated to (prolly 14-18psi on that FP Green). You can also just jumper the boost hose directly to the wastegate for minimum boost, but the spring still is the factor.
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