What kills it for me is the `Command + number` shortcut - that triggers bookmarks instead of tabs (like in Chrome or FF), a setting that can't be overridden :/
Even if an app doesn't have an override for chosen key assignments, you should be able to override anything visible in a menu by using System Preferences (Keyboard category, Shortcuts tab, App Shortcuts item).
Like you say, in the end, the point is, Safari would be a much better browser if it's UI was much more customizable. Of course, that's completely against Apple's idea that they know how it should look, and if your opinion is different, it's simply because you are an idiot. I really wish they would back away from that attitude, and allow more customization.