Well, actually this is not to handle war overlays, but web resource filtering. Ex. you would want to deployed the filtered web.xml not the raw file in src/main/webapp. Only way to do that is to declare generated resources first in .settings/org.eclipse.wst.common.component
We'll see with WTP 3.2.5/3.3.1 if the fix for https://bugs.eclipse.org/bugs/show_bug.cgi?id=353834 helps with this issue.