The pdf outline tab is a great feature and it is already incorporated.
It would be fabulous to use this collapsable outline to structure and easily navigate lengthier notebooks. For instance for study notes this would be more than helpful.
On the other i could often use these little red flags as bookmark signs like other apps have (bamboo paper, notability and most ebook readers). This is faster because you dont need to specify a bookmark text, you can unmark easily and you have a visual clue in the thumnail preview.
The bookmarks tab could then be used to show thumbnails of all pages with such a bookmark flag.