Most digital logic outputs will have either a slight negative or slight positive voltage, it’s simply due to component tolerances. The only way to compensate for this would be to have a trimmer for every single output, which would add a fair bit of cost, board space, and calibration time. The reason this isn’t done is that for most applications it doesn’t matter because gate inputs only look for voltages above a threshold of over 1V.
If you’re feeding a gate directly to an analog input it then it may have a slight effect. In a lot of cases this doesn’t matter either, but if you’re controlling an audio level and recording something as your only sound source it could be a factor. On the Quad VCA this will be particularly noticeable in exponential mode. Another thing you can do is feed the gate out to an envelope such as the Quadra first, and then use the envelope to control the VCA. This will also have the added benefit of allowing you control over the rise and fall times as opposed to having an abrupt on or off effect.