I agree with you! I personally don't use these writing programs. I know that they can help with grammar and punctuations, but I think they remove that "special touch" your story would have. After all, it's your story, and in my opinion, when you use programs like Grammarly or ProWritingAid to "improve" your chapters, the style of writing you put in your chapters would just... fade away.
Honestly, I think your satisfaction with your chapters is more important than punctuations. If you write chapters without using any writing programs, it kind of makes you feel great, and you would get really motivated as well! (although I don't know if every author feels this way, but I do)
As you can see when you use these programs, the suggestions in Grammarly or any other writing software aren't quite accurate; what I mean by this is... they don't wholly understand your story. If you're focusing on something heavy and emotional on your story, they would still correct your grammar, but they can't help you highlight the impact you really want to bring to your audience. These programs can definitely help you with your grammar, yes that is true, however, they can't help you emphasize your story. They can improve your grammar, punctuation, and sentence structure, but they can't really help you with your novel itself, if you get what I mean.
It's just like what they say, no one knows your story more than yourself.