As reasonable as it may be to suppose that H. fell not once, but twice from heaven, we have to admit that no ancient author ever attempted to rationalize the contradiction that way. And you’re right, it is a contradiction in the Iliad : 1.590ff. has him thrown down by Zeus, while eighteen books later we have the passage you cite, in which his mother pitches him out. I see no way out of simply accepting the contradiction; it’s not the only one in the Iliad: Bonus dormitat Homerus.
I agree, however, that the Book 18 account is not an alternative version of why Hephaestus is a cripple. As Nilsson points out (GGR 1.527), Homer’s Hephaestus limps in both legs — there is nothing to indicate that only his foot is crippled. The fact that Zeus grabbed him by the foot when throwing him may have nothing to do with his handicap. And the fall onto Lemnos in either case, while heavily injuring him, may not have been thought to be the cause of his lameness. Here’s why:
In myths of a number of cultures, blacksmiths, whether divine or human, are strong but distorted creatures — dwarves, cripples, etc. Presumably this derives from the blacksmith’s reality, having to spend his days exerting his arms and shoulders while standing stationary before his forge or anvil. Huge chest and arms, but weak, spindly legs. Conversely, it has also been suggested that those who were lame from birth might tend to go into such a profession, just as blindness might push one into the rhapsode’s trade. So Hephaestus’ handicap, like Homer’s blindness, might simply have “gone with the territory” in his professional capacity, and might not have required an aetiological myth.