I'm running kitty with multiple main windows in one instance and listening on UNIX socket (--single-instance --listen-on unix:/tmp/mykitty) and trying to control it remotely (@ --to unix:/tmp/mykitty) from outside. I noticed the following inconsistency when running remote commands: set-font-size changes font in ALL windows but set-background-opacity only affects one window (I guess the first one opened).
When sending remote command from inside one of the windows, set-font-size affects ALL windows and set-background-opacity affects only current window.