I "fixed" this with a Hammerspoon snippet that monitors input changes and reverts them:
programs.kitty.extraConfig = ''
include ${config.xdg.configHome}/kitty/temporary.conf
'';
Then my ~/.config/kitty looks like this: ~/.config/kitty $> ls
87 Dec 13 11:39 kitty.conf -> /nix/store/....-home-manager-files/.config/kitty/kitty.conf
381 Dec 13 11:42 temporary.conf tree: aliased to echo '2\n3\n4\n5' | fzf --preview='exa -l -T -L {} --git-ignore' --reverse --preview-window down:99% --bind 'j:down,k:up,q:cancel,enter:cancel'