I never gave it a second thought because I saw it in print that way and have always written it that way.

I get now the inclination toward deep-seeded as a metaphor, but if you think about that it makes no sense. If you plant a seed deep, it won't grow at all, I mean the plant will sprout under the soil and you'll have nothing.

Deep-seated means that the position is fixed, that its place would be difficult to remove without serious effort that would go beyond the action of simply moving its position above the ground.