Suppose you have deps.edn at the root and then a bunch of sub-directories with their own deps.edn files.
If you want to have a set of common dependencies for all of the projects, you can simply have e.g. a common directory where common/deps.edn specifies all of the common dependencies and all the rest of deps.edn files list common as one of their deps.
However, that doesn't work with org.clojure/clojure, making it implicitly special.
As I mentioned on Slack, it seems that clojure.tools.deps/root-deps brings the default top-level version of org.clojure/clojure and nothing else can override it but another top-level version.