My PhD advisor is writing most of an article without considering some of my inputs
I do not know whether this could be an answer to your question or not. 

I find it completely normal, especially because it is your first paper. My advised changed 99% of the first version of my first article, and when I read now what I wrote, I laugh about it because it was really low quality. Of course, this is normal because I was new in writing papers. My advisor did not even explain the changes. Instead, he said: "check my revision, and you will learn how to write papers".  Now his revision does not exceed 1%. 

Back to your case, I think, your advised found that this paper has a high potential to be accepted, and he wants to increase the chances. Even if a scholar did the experiments by himself, the adviser has an experience of many years in writing papers. In the first paper, we usually try to write all the details, believing that they are all important. In most cases, what is important for a scholar is a part, which took more time. On the contrary, an experienced researcher knows what is important and what is redundant.

Overall, It is too early to disagree with your adviser about what to write, where his experience makes the difference. Try to follow him and if you are right, the reviewers will prove it. Otherwise, you will learn from your mistakes.