I think there's a substantial difference between what WildFly includes and what other projects produce: WildFly is the reference so they can define what "main" means, but if all other projects also start producing modules using the "main" slot then there could be conflicts.

In the specific example, there might be other projects who also want to introduce a org.parboiled module and they might not be aware of our module (like we are not aware of theirs).

However, other projects can hardly ignore what is in WildFly already: that's very well visible so unless you intentionally want to replace a core module, that might be wrong but at least one will be aware of it.