Back about 22 years ago, I did a scrapbook layout using silk azaleas and dogwoods. That was long before they had flowers for scrapbooking. These are not in page protectors, but the book has been stored standing upright, like a book in the library. When I open the book to the page, they bounce back to their original shape every time. No sheet protectors in that book.
Over the years I have also used a lot of what we used to call "lumpy stuff" in my books, and they only thing I am careful about is not to put them directly across from photos that could be dented or scratched by the opposing embellishment on each side of the page.
I try not to go thicker than 1/4 to 1/3 inch and no sharp edges. If I have a brad that I use, I often tape a piece of cardstock to the back just to be sure.
You can also cut the page protector and let the embellishment peek out from the protector. But standing the books on end takes care of most of the problem.
If you do a lot of these thick pages, you need to have a book with a spine that is expandable unless you are using a 3 ring book.
Diana at www.scrapbook-advice.com