Neglecting the CO will absolutely be a problem. The material properties required for handling hydrogen are very different than those for other gasses, especially methane. Increasing the concentration of hydrogen significantly increases the difficulty.
But if the pressure of hydrogen was the same as the partial pressure of hydrogen before, wouldn't it be the same? I mean, if the materials could stand that partial pressure, why wouldn't they be able to stand that pressure in the absence of CO?
Unless of course that actually took it below atmospheric pressure so all the forces went in the opposite direction.
[1] Actually "town gas" which was a mixture of hydrogen and carbon monoxide. But I imagine not including the CO would not be a problem.