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HI and thank you for your question.
Using the glass tube allows you to see the fuel level inside the float bowl. Therefore, the fuel level should not change just because you raise or lower the tube. You are not altering the fuel level inside the float bowls by moving the tube so it isn't going to change. You can move the tube up and down so you can get the graduations set to make it easier for you to read the MM. The fuel level spec from Yamaha is actually 10.5~11.5 mm above the line cast into the outside of the float bowl. The 0.1mm is so insignificant it isn't worth worrying about. If your fuel level is between 10.5~11.5mm above that line then the fuel level is correct. Be sure you synchronize your carbs too. That is a major factor in how the engine responds to throttle and bottom end acceleration.