If you want your book to be entirely under your control, then that's what self publishing is for. If you want your book to have the benefit of a team of people who know the industry and how to sell books, that's when you submit it to publishers.
I can't tell you the number of queries I get that specify what the book should look like, the trim size, the layout, and often the cover. I can't tell you because those queries don't even reach the query bin, they're pretty much instantly rejected.
The brutal reality of publishing is that the contract you will sign when I sell your book gives the publisher complete control over all those things. I can often negotiate the phrase "with consultation, approval not to be unreasonably withheld" into the contract, but in the end, the publisher decides what the book will look like.