dino
Here is what I am noticing. Safari chooses from the Favorites, not the Bookmarks.
I would suggest that because when opening a new tab, you see the list of Favorites and it is easy for you to see what number you want to launch. The bookmark bar is hidden, displaying it opens a new window.
I also tried to copy the favorites to the bookmark bar and it seems that you cannot, they just move. I guess that makes sense since users would not want to duplicate them.
For now, I will manually add my favorite items to my bookmarks in the same order so that I can use the shortcuts. It is not ideal.