Correct me if I'm wrong, but I think this limitation wrt Makefiles is entirely a choice by CMake, or at least a lack of volunteers for adding support to the Makefile generator. Ninja itself doesn't have any support for C++ modules (see https://github.com/ninja-build/ninja/issues/2457). In fact, Ninja has fewer features in that regard than plain Make as Ninja requires all dependencies to be statically defined.