So, you’ve never had two different targets that depend on something in a subdirectory? If you’ve just solved this by building subdirectories in a specific order, or building entire subdirectories rather than the specific targets you need, what you’re really doing is making an incorrect dependency graph in order to work around make’s limitations. These kind of decisions make sense for full builds, but interfere with incremental builds.
Bazel & family (Buck, Pants, Please, etc.) are among the few build systems that solve this problem well. It’s not an accident that they all use package:target syntax for specifying targets, rather than just using a path, because this allows the build system to determine exactly which file contains the relevant build rule without having to probe the filesystem.
I would love to simply recommend Bazel but the fact is there is a bit of a barrier to entry depending on how standard / nonstandard your build rules are and depending on how you think that third-party dependencies should be pulled in. Depending on your project, you could convert to Bazel in an hour just by looking at a couple examples, or you could have to dive deep into Bazel to figure out how to do something (custom toolchains, custom rules, etc.)
As you observed, the alternatives to make are often inferior, and it’s often because they’re solving the wrong problems. For example, sticking a more complex & sophisticated scripting system in front of make.