How does MacPorts work with /Applications/MacPorts and /opt/usr/local/bin
The different install paths does not have a consequence here. It doesn't matter where the application is installed in terms of running under X11 or native OS X.

kitty on macOS is a native macOS application, and is not "managed" by Xorg. You do not need Xquartz, Xorg or X11 at all to run kitty on macOS.

i3 is a window manager for X11. It will only work with and affect X11 applications. You will not be able to use it as a tiling window manager for native macOS applications, such as the default kitty.

In order for kitty to be managed by i3 you would have to recompile kitty using an X11 backend, if that is possible. The X11 backend is already made as it is used on Linux. However it doesn't seem like the X11 backend has been tested on macOS, as the author intends the user to use the native Carbon backend.

Another solution would be to install a macOS tiling window manager such as chunkwm with skhd. That window manager would then be able to tile windows of both native macOS applications as well as the ones managed by XQuartz for example.