IMO this is Eclipse JSF Faces Config Editor isssue. It just doesn't aware of that several web-resource nodes are normal use case. JBoss Tools in this case iterate over all mapped resources to find right one. In your example JBoss Tools would pick up /src/main/webapp path from two mentioned here, no matter waht is the order of nodes in org.eclipse.wst.common.component.
This is fixed in JBT 3.3.0M4 (https://issues.jboss.org/browse/JBIDE-9753). You'll need to use Eclipse 3.7.1 (SR1) and m2e-wtp 0.14.0 (See https://bugs.eclipse.org/bugs/show_bug.cgi?id=353834 and https://issues.sonatype.org/browse/MECLIPSEWTP-168)
Basically, a new tag="defaultrootSource" should be added to src/main/webapp, to deal with multiple source roots in .component. Running "Update project configuration" should add it automatically.
you can use a nightly build of JBoss Tools from http://download.jboss.org/jbosstools/updates/nightly/trunk/. or wait a couple weeks for the official release of 3.3.0.M4