I noticed there is an old version of m2e-apt in JBDS TP 4.40.0.Beta3 which will be released with JBDS 8.0.0.Beta2.

http://download.jboss.org/jbosstools/targetplatforms/jbdevstudiotarget/4.40.0.Beta3/REPO/features/org.jboss.tools.maven.apt.feature_1.1.0.201311290819.jar

In JBoss Tools TP, we have the newer version:
http://download.jboss.org/jbosstools/targetplatforms/jbosstoolstarget/4.40.0.Beta3/REPO/features/org.jboss.tools.maven.apt.feature_1.1.0.201405210909.jar

This update was done in JBIDE-17306 .

The thing is that for JBDS, the updated feature is already included in JBDS installer / update site. So it seems the one in the JBDS TP is a left over ready to be removed. Or if it's needed, it should be updated to the newer version (or rather build).