> There is the "windows" key of course for the last few decades but somehow using that as a modifier never caught on in the Linux world.

In the window manager side of linux, Super ("Mod4") is often used for the windows manager level keybindings.

As for the configuration thing, those things are usually checked in into the dotfiles. So you've done it once four years ago, and you never think about it again. iterm2 is nice, but I'm not sure about the ergonomics advantage for a power user.