My PhD advisor is writing most of an article without considering some of my inputs We are currently writing a first article with my PhD advisor. The research was mainly designed by him; I performed all the experiments and found a model to explain the results.

The article is soon to be finished. I am supposed to be the first author of the paper but at this point, I am more and more considering to ask my advisor to put me as the second author or maybe even ask to have my name removed.

My advisor wrote most of the article, which I already find weird given that I am the first author. This is not due to my lack of initiative, I've been explicitly told not to write some parts. It really feels that I am simply a secretary asked to check for typos, formatting issues, and to make graphs and figures as he sees fit.
When I correct some of his writing, he sometimes takes into account what I propose/correct, sometimes he disagrees and explains why, but sometimes completely ignores it (my comment is deleted and not addressed). Some of these ignored comments are not fundamental, but I find some others very important and I am really not comfortable with some parts of the manuscript (he knows this given that I wrote it in the comments).

As an example, my advisor is very excited by a small theoretical model I proposed to him once that could roughly explain the experimental results. Yet there are still gaps and unsupported hypothesis. He knows that I am very reluctant to make this modeling an important part of the paper (which otherwise present both qualitative and quantitative experimental evidence of phenomena not previously reported), but this is now becoming more and more important and is almost the central part of the article. We discussed that once, his answer was simply that I should be proud of myself to have explained something rather than be too critical. 

Other examples include him writing something along the line of "when XX was observed, we systematically found that this was due to YY". Something I actually only observed once and I am not confident that it can be so easily generalized.

My question is simply how to deal with that. My relation with my advisor was great but it is becoming more and more strained (especially from my side) as this article evolves. Is this a regular flow between a student and its advisor during the writing process? This is a long, in-depth >30-page article, if this information can be useful. With my Master advisor I had written and published a short-letter (4 pages), and I was completely leading the writing.
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.