This is only vaguely related, but I have a similar setup, except that I start i3 from a home-manager managed xsession.
Instead of services.xserver.windowManager.i3.extraSessionCommands
I’m using:
xsession.profileExtra = ''
eval $(${pkgs.gnome3.gnome-keyring}/bin/gnome-keyring-daemon --daemonize --components=ssh,secrets)
export SSH_AUTH_SOCK
'';
…after which it almost worked, but was complaining with Gcr: couldn't prompt for password: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.gnome.keyring.SystemPrompter was not provided by any .service files
when trying to access the prompter.
“Fixed” that by adding the package gcr
manually to my system packages.