Personally I'm +1 on allowing any project to have a modules section. This used to be allowed in early versions of m2.
That would fix this limitation.
Also, it's no longer a problem with eclipse. Right now you can't add pom.xml projects to eclipse, unless you
specify a workspace somewhere which will link project files.
It might not work to allow this currently, though, because of cyclic dependencies.
Why was this disallowed? I can't seem to find the reason in Jira.