When setting the Bookmark Toolbar to only show on New Tab, when you switch between a new tab and another tab (say, youtube for example) you can see the website adapt to the new size .
It would be better to keep the sites at their size without the Bookmark toolbar in the background to not see this adjustment.
One way that might work is to have the Bookmarks Toolbar drop down and overlays the top of the new tab page so the toolbar area remains the same size.
Or build it into the new tab page? (I think a lot of people would like to have it in the page if it allows multiple rows so they can see more items.)