 ::Only at higher order.  The direct effect of Uranus on Neptune, for example, doesn't depend at all on Neptune's mass.  It's only when Neptune perturbs Uranus, which then causes a slightly different perturbation of Neptune, that Neptune's own mass enters into it.  That's a tiny, tiny, tiny effect. ::The real reason here appears to be that the residuals in question were not in the orbit of Neptune but Uranus, which was much more well known at the time.  They were actually using observations of Uranus going back to the 1700s, while Neptune had only been known for less than a century.  Neptune was more massive than thought at the time, so the Uranus residuals were calculated based on a too-small Neptune.   