From my observations, it's quite rare to see developers' personal "project files" in a project's source tree or checked into VCS. Even a Geany-specific project like geany-plugins doesn't contain a single project file in its repository (from a quick `find' for *.geany).
Yes, agree, its only been useful for projects that define non-default build commands or settings. Then they need to be stored with the project to ensure that the developer uses the correct commands when they open the project.
Cheers Lex