You are correct. If you run the co2 through your INTAKE the carbon in the filter will absorb the carbon just as it absorbs other toxins. It is actually recommended to remove the carbon from the filtration when running co2, so long as the other media has had adequate time for beneficial bacteria to generate.
That being said, I have my co2 injecting into the RETURN line. I tried posting a picture but it will only post as an attachment, I hope you can see it. It is then fed through the spray bar and inject straight downward with the flow so it takes long for the bubbles to reach the surface. This allows more of the carbon to be absorbed into the water.
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