If you have to do make clean in a monorepo you are pretty much toast. Tooling for impact detection and reliable makefiles that always succeed incremental builds is absolutely crucial.
In a way this is one of the hallmarks of a monorepo - Interfaces and dependencies changing so quickly it becomes too troublesome for humans to categorize (and re-categorize) them into repositories, so you let a machine (makefiles) do the work instead. And even without a monorepo you still have the same problem, eventually you will have to integrate all your mini repos into one final product, which you want to have tested. This is something you want to do as frequently as possible, ideally on every commit, not by doing major version-steps of sub-projects.
In a way this is one of the hallmarks of a monorepo - Interfaces and dependencies changing so quickly it becomes too troublesome for humans to categorize (and re-categorize) them into repositories, so you let a machine (makefiles) do the work instead. And even without a monorepo you still have the same problem, eventually you will have to integrate all your mini repos into one final product, which you want to have tested. This is something you want to do as frequently as possible, ideally on every commit, not by doing major version-steps of sub-projects.