A fetus doesn't have control over another body either, a woman can still do what she wants when pregnant.
A person can still do what they want with one kidney..
I mean, firstly, don't be silly. Pregnancy is a relatively extreme medical condition. It affects a huge range of bodily functions. I don't know if you've ever spoken to someone who has been in the later stages of pregnancy, but it's incredibly debilitating. A person cannot do whatever they want when pregnant. Often they will struggle to do much at all, which is one reason why maternity leave exists. Historically, pregnancy and childbirth was also a major cause of death in women. Pretending its in any way unreasonable to not want to go through pregnancy isn't fair.
Secondly, the foetus doesn't control its mothers body, but it does impinge on its mother's medical control over her own body. It literally lives inside that body, it forces that body to change and adapt to its presence without consent, it may ultimately kill that body. The issue, fundamentally, is that the body
is a person who possesses intrinsic value and rights
. They are not an incubator, or a vehicle, or a tool. They are a living human being.
Did you not notice that the pro-choice side is in defense of the "there isn't a soul yet" position? Rephrase it to unconscious, or doesn't feel pain, or whatever humanizing thing you may think is relevant. The framework of "early abortions are fine but not after so many months" is the idea that at some point an abstract change transforms a fetus from a parasite into a person, and it was justified for centuries in religious terms. Changing the words to not say "soul" doesn't make the position more or less correct.
I think you've fundamentally misunderstood what the basis is for the restriction on late term abortions. It isn't meant to protect the consciousness of a developing foetus, that's not even a factor in the decision making process. The determining factor which is used to legally limit abortion, in the vast majority of secular countries, is the line of viability. That is to say, the point at which it becomes reasonably possible to potentially keep a foetus alive to term outside of its mother's body. It is entirely possible to abort a foetus after this point, and it does happen in some cases when it is deemed appropriate, but the medical ethics of doing so are more complicated and may involve complex medical decisions and balancing conflicting principles and priorities.
That is why we limit abortion. It's not because we believe in some magic point where a foetus becomes conscious or develops a "soul", it's to protect the people who perform abortions from difficult, stressful or ethically challenging decisions regarding whether or not to keep potentially viable foetuses alive. It is an unfortunate side effect of the fact that medical knowledge and technology is now extremely good at keeping premature babies alive far, far past the point of natural viability.