I don't see a significant difference.
The fathers decisions did not lead to the child's kidney failure
Choosing to have sex is not choosing to become pregnant. Birth control does not always work. If you still persist in this view even in cases of unintended pregnancy, you're essentially saying that giving up your bodily autonomy is the price you pay for having sex. Do you really believe that?
Choosing to have sex, is choosing to risk pregnancy. There is nothing to believe or not believe there, that is an objective fact.
Anyway birth control works well enough it's safe to assume that the arguement over abortion isn't solved with 100% effective birth control.
And even if you do, why does this obligation to give up your bodily autonomy to preserve the life that resulted from having sex end at birth? The father's decision to have sex led to the child existing, and the child will die if the father does not give up his kidney. Is he legally obligated to give up his bodily autonomy to preserve the life of his child? The simple fact is that no, we don't do that. Similarly, a mother isn't legally obligated to give up her kidney to preserve the life of her child with kidney failure either.
It ends at birth because child now has its own autonomy. The kidney failure wasn't a result of decisions made by the mother or father. This analogy still does not hold up.
As far as I can tell, you need to pick. Either we should start legally forcing parents to undergo surgery, or we shouldn't legally force women to go through pregnancy. Children are clearly at least as important as fetuses, and yet we don't force fathers to give up their bodily autonomy to preserve the life of their children. If you argue that women should be legally obligated to give up their bodily autonomy to preserve the life of a fetus, then why does that obligation suddenly end at birth? Are fetuses more important than children?
That's a false equivalency. The fetuses condition is a result of a mother and fathers personal choices, not an uncontrollable condition such as the kidney failure. And no we wouldn't force the kidney exchange if it was because the US court cannot sentence people to be dismembered, but they can prosecute you for causing kidney failure.
are two separate autonomies (is that a correct plural?) from the start.
I don't know what you mean here.
At no point are these two the same autonomy so they don't suffer the same moral dilemma.