The CLI and Inkscape use independent sets of parameters. If you’re using the same version (2.5.x) in each, then the values are set the same way, but you would need to set them.
If it might be paper/machine flatness, I would suggest that you test your pen up/pen down positions in the four corners of the plot area as well as the center (for example, on top of a thin piece of plastic or paper that will not bleed through) to ensure that you have the required range.
