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You are confusing fully re-calibrating the gyroscope to re-calibrating it to remove drift. When you set on the table to re-calibrate, you are resetting where it considers the x y and z axis to be. What the IR sensor is doing is accounting for a slight error that grows overtime which is gyroscopic drift, which is why the Switch games need you to re-calibrate every once and a while. The IR sensor basically used the ir sensor to find the slight offset from where it expects it is, and re centers it. using the same initial axis calibration.
For World of Goo and the other Switch games, you just manually recenter the controller to where you want it to be pointing to the center, press a button, and it resets it to be centered, kind of like how it works when using motion controls in Splatoon 2. Both are re-calibration though, just different levels of it.