Yes McGrath, I think you're right. It's all in the way the line is heard rather than the logic of it. Also maybe it's that "....the Woman's conquering seed...." implies ownership by her somehow. And does it depend on a man's relationship with his mother how he feels about that, I wonder?

Cats, Is "Harky" a contraction of "Hark Thee"?

Joe F, yes I've always been quite taken with that particular Biblical/mythological image in the "Battle Hynm of the Republic". Always a bit sad for the serpent though. They do get such a bad press. The ones around here are terrified of being stepped on. Maybe they scare each other by singing that line at snake gatherings.
Cheers, Joy