From the bottom a slight misalignment wouldn't be as noticeable, and given the shape of the Nomad with the low slung engines and down curving engineering hull and the slightly arced shape of the saucer it may even be an acceptable feature.
All other saucers line up correctly with the Nomad hull, except in areas where hull and saucer contours don't match, the problem is that the Nomad saucer sits just a little too high on it's "hardpoint". It's not a game breaker, I think the Nomad looks cool even as it is, but if one of the artists wants to give it a little tweak it would be much appreciated.