This is only relevant for cases where the requireAllDefinedDependencies() is used.
In that case, the metadata needs to be provided to the transform, but Gradle does not provide a direct mechanism for that. Hence, we provide all the metadata we have from a configuration. This can be configured as documented here.
However, even if you combine all your scopes into one module path, there is still information missing: From transitive dependencies, you typically select the runtime variant. Then, dependencies that are only in the api variant – compileOnlyApi dependencies as published by org.apache.logging.log4j:log4j-core – are still missing.
The best way to deal with this at the moment is to not use the requireAllDefinedDependencies for modules for which you know that they only appear on the compile module paths.