Even if you change the webAppDirName property in a WAR build, the WST file still sets it's deployment path to src/main/webapp. Looking through the source code I found a TODO saying that it was not being evaluated lazily, so this seems to be a known issue.

build.gradle

apply plugin: 'war'
apply plugin: 'eclipse-wtp'

sourceSets {
main

}

webAppDirName = 'WebContent'

.settings/org.eclipse.wst.common.component

<?xml version="1.0" encoding="UTF-8"?>
<project-modules id="moduleCoreId" project-version="2.0">
<wb-module deploy-name="war">
<property name="context-root" value="war"/>
<wb-resource deploy-path="/WEB-INF/classes" source-path="JavaSource"/>
<wb-resource deploy-path="/" source-path="src/main/webapp"/>
</wb-module>
</project-modules>