Because you included a third-party project into your build which is not compatible with your build system and you don't want to rewrite all their ninjafiles into makefiles to match.
Someone should really formalize a standard for declaring dependencies which build systems can share between each other.
A “standard for declaring dependencies” is, itself, a build system without the execution engine. The execution engine is not actually the hard part about making a build system. So, what you’re asking for is really just a standardized build system.
Because it can be hard to maintain non-recursive make systems for large projects. Just because recursive make is discouraged does not mean that the alternative is without its own drawbacks.