I don't think that changing "Show bookmarks bar" to "Always show bookmarks bar" will clarify the behavior. Because you will have the same issue, "Always show bookmarks bar" will be UN-checked but the bookmarks bar will still be shown on NTP. So for that button a name like "Show bookmarks bar on non-NTP pages" :)
(which doesn't sounds good and it's too long), will reflect the actual behavior better. Maybe somewhere in some FAQ page this should exist: "Bookmarks bar is always shown on New Tab page", if this is indeed expected
(no code changes will be needed).
Imagine I want to do a screenshot/screen share and I don't want people to see my bookmarks. I don't have a way to do this on NTP page. So it would be nice if we could hide it there also.