The issue is that when :refer :all is used, clj-kondo cannot see statically which vars are brought in, unless dependencies are linted as well. In Calva this happens automatically, if you open the project at the root where a deps.edn or project.clj is located, upon which clojure-lsp will calculate the classpath and lint all dependencies on the classpath using clj-kondo. After that, the vars brought in via refer :all are resolved correctly.
When opening this specific project in the root, it won't have that effect, since there is no deps.edn or project.clj. Opening the project in the directory e1 does work.