Why can I not set Safari keyboard shortcuts? Conflicts with secondary, unlisted Back/Forward commands
It seems like this is a widespread issue. I tried redefining shortcuts such as creating new windows, but although the shortcut appears in the menu bar it doesn't actually work—Safari uses the default extension. This happens for other Safari menu bar items as well.
Sadly this doesn't seem to have been fixed even on Safari 14 (shipped with macOS Big Sur).
In order to overcome this strange limitation/bug, I use BetterTouchTool to set up custom keyboard shortcuts, and it works pretty well.