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I haven't really used bspwm and sxhkd, but from nixpkgs it seems all the inputs from *.configFile just get used in a command such as $ sxhkd/bspw -c . So I'm guessing, if it's possible to run a complete config through a single command, you should write it up like such and not like the actual config file. It probably just works with bspwm because its a single command.
Personally I'd recommend using home-manager for such actions. Then you can actually declare each aspect of the config and add extra config if needed.
I highly recommend the home manager config for this. My sxhkd is in .nix/hosts/lemon-tree/config/sxhkd.nix in https://github.com/PassiveLemon/lemondots if you need a reference