With the standard templates, a newly created project will reference the NuGet packages for MonoGame.Framework and MonoGame.Content.Builder.Task.
Or did you modify the templates to reference your modified MonoGame assembly?
You can remove the NuGet references after creating a project, and reference your modified version of MonoGame instead. If that’s what you want, this tread should help you do that.
It’s not you. The docs are thin, especially in the build from source department.