It's impossible to depend on a deps.edn-based project using git or local dependency when that project uses custom maven repos. Attempts to build classpath for projects depending on such projects will fail.
I created a minimal repo that illustrates the issue: https://github.com/vlaaad/deps-mvn-repos-repro
It contains 3 deps.edn projects: lib, app-local and app-git.
lib contains a single deps.edn file that defines a custom maven repo and a dependency that pulls from that repo.
app-local contains a single deps.edn file that defines a :local/root dependency on lib.
app-git contains a single deps.edn file that defines a :git/url dependency on lib.
clj -P should succeed in lib, app-local and app-git projects.
clj -P succeeds only in lib and fails in app-local and app-git with the error "Error building classpath. Could not find artifact net.sf.saxon:saxon-dom:jar:188.8.131.52 in central (https://repo1.maven.org/maven2/)"