It was also new to me that deploy-rs is in Nixpkgs.
I guess if you want to specify your own deployments, you still need to import the flake (is that so?). However, for the executable you can use the version in Nixpkgs! I guess the advantage of the Nixpkgs version is that it will be pre-built and more stable but updates may lag behind.
So what I do now is pretty ugly; I needed the library code for the activation, but it included a reference to the deploy-rs in the flake, so I copied that to my flake and changed it to use the nixpkgs deploy-rs instead.