Resource.Embedder itself uses the core package to do the actual embedding.
If you have a custom workflow that doesn't quite fit with resource embedder you are free to use the core package to embed your own files.
By adding the NuGet package to an assembly it is possible to manually inject resources and code into other assemblies.
See this code for injecting resources and this code for injecting code.
When a user drags a file onto an exe the exe can embed the file into itself.
I have used this in the past to embed plugins with the exe.
That way I can build the components seperately and then ship different versions of the same exe to various customers, each preconfigured with certain plugins (without having to recompile or distribute multiple files).
While you could directly reference the default plugin in the main project.
Based on user workflow it may be necessary to store settings/files. Usually this is done in a seperate file next to the exe (or in a seperate data dir).
By storing it in the exe, you would ensure that the settings always travel with the exe and that multiple exes with different settings could exist.