Yep, I think you got it and JBIDE-9788 looks to outline the issue, I'll track that JIRA for resolution.
The metadata bug JBIDE-9787 I have seen for some time and I hope you guys move away from that as the default config with the final release of JBDS5. Storing the deployable EAR or WAR in an eclipse metadata folder always gets out of sync with the server especially if you are changing server configurations outside of JBDS. We have always switched that to "use JBoss deploy" folder for previous EAP servers like 4.3 and 5. Not sure what the correct answer is for JBossAS7 and EAP6 though.
I do get some of the AS7 runtime libraries from <JBOSS_AS7>/modules/javax when I assign the runtime library to a project. I just had issues with both JSF 2.0 and JSF 1.2 libraries being on the classpath. This all might be interrelated though.
Robert