I also found that very uncomfortable. I was very annoyed about sex Ed also only teaching contraception for straight sex and tech classes using male and female terms to describe plugs. There are other words, so I exclusively used them as a small rebellion.
Idk if you can do much more than talking to your teacher. If you get along with the other trans students or there's a diversity committee at your school, maybe you could bring it up with them.
I had such a hard time during any class that talked about chromosomes! I remember being surprised by just how much it affected me, and all I could think about was how I would never have a Y chromosome. I could barely pay attention to anything said during the class, and I cried in class a few times.
I don't know that I have any advice, but I just wanted to say that you are definitely not alone in how you feel, and while not every trans person may be affected the same way, your discomfort is completely understandable!
This one is special:
I'm a researcher in the biological sciences, and more specifically, part of my research focused on sex-specific outcomes. I've also taken a lot of endocrinology courses and genetics courses as part of my training. In other words, I've been confronted with a lot of information about how sexes differ, and I've had to come to terms with it. And oddly enough, over time, I've come to be really fascinated by it!
Here is my advice; try to remember that the biological reality of sex that you read about in a textbook is FAR removed from human manhood or womanhood.
All sex differences exist because they were selected for by natural selection. Sex only exists in nature because it perpetuates genetic material. And how sex differences occur vary between species and reproductive strategies. That's why not all species have XY and XX chromosomes. Not all species reproduce sexually, either. It depends!
But the point is, sex differences developed for the same reason that bats evolved to have wings and fly.
There's no deeper meaning to the existence of sex or sex differences beyond increased reproductive success.
Now, what does that mean for us as humans? Well, as you might've noticed, humans have moved beyond nature in many ways. We are able to give meaning to who and what we are. We are not baby-making machines, nor are we consciously aware of the fact that our alleles are optimized for spreading our genetic code.
This is for better or worse. Humans are the ones that made social "rules" that associate with our sex characteristics. Even ones that we wouldn't even know exist without education (like sex chromosomes!). But this also means we can choose to dismantle these social rules or educational imprint.
What you need to remember is that some sex differences are malleable (like those caused by sex hormones), and others are something that we can't change, but do not have a direct effect on our daily lives (chromosomes).
Another thing that has been comforting to me is just taking a step back and removing myself from the situation as I learn about these topics. Let yourself just learn! A lot of it is actually interesting. And there's tidbits about my sex differences that I actually appreciate. For example, as you learn about XX chromosomes and their role in evolution, you will find that the XX chromosomes are actually the most "complete" version of the human genome and create a strong, robust system that is pretty admirable. In other words, XX chromosomes are just cooler, for reasons that are hard to summarize in one reddit post...

But anyways, I hope that you'll be able to get through this class okay. I realize how uncomfortable it can be and wish you the best of luck!