> I increasingly feel like build systems should never be relying on any "native" utilities from the host system, and should instead be bringing them in via dependencies.

Well, you see, while this, frankly, applies not just to build systems but to most of software, the consensus in the community of distro-maintainers is that it's actually wrong: you should use your system's package manager, and tools it can install, and let it fiddle with the ambient environment and give you that delicious "path dependency". And if your distro's packaging environment doesn't allow to do the things you need (e.g. being able to install both mongodb 3.8 and mongodb 5.0, ideally at the same time, but okay, I can keep running apt remove/install over and over, but I do need to check if my app correctly handled the wire protocol changes), well, that's your problem for desiring strange things.