A motor hooked up to an Auto transmission will typically work differently to one hooked up to a manual (Some motors have different power ratings between "auto" and 'manual" types).
A manual gearbox has a solid coupling to the engine (with clutch engaged) , whereas an auto has a little more "slip". so the engines may run differently (for example) going down hill with the throttle closed.... the manual may require less fuel to keep running smoothly in these circumstances compared to the auto. If the same ecu was used with both transmissions, one may run richer (and there fore use more fuel and create more pollution ) than necessary
The difference may not be only in the ECU, some auto engines have milder cam timing than their manual counterparts (hence less power, but sometimes more Torque in the A/T engines) .
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