I'm not a huge Mail user so I'm not up-to-speed on keyboard shortcuts. But I was able to navigate with the keyboard easily — I hit tab to focus on the correct list then use the up/down arrows to select the inbox or message (your 4/5/6). After hitting Cmd+W both Cmd+0 or Cmd+1 bring the Mail window back for me. And Cmd+Shift+D still sends mail which is the main one I use
I am a huge Xcode user and primarily use the keyboard for code navigation, and that is as good as ever on the 13" MacBook Air in Big Sur. Also use Sketch a lot, and that has been just great too
I guess we have a very different perception of Big Sur but mine is generally favourable, and I don't see the wasted space that you see. There have been a few weekends where I have done all my work on the 13" MBA, which is only just now possible due to battery life, and the experience has been really, really nice