You should be able to put the netlify.toml in each subdir, if the base is configured in the UI, yes.
If you have one in the root that doesn’t have base set, that should be fine. If base is set it in, and doesn’t match what’s in the UI, not sure what would happen (so, don’t set base in that netlify.toml unless you have only one netlify site, is my suggestion).
Does that help?
I will also review this feedback with our documentation team who are working specifically on the monorepo docs this sprint.