Max,
The defaultRootSource value is added automatically when the JavaEE Facets are installed in WTP 3.3.1/3.2.5/3.4.0
Since m2e-wtp messes with the virtual folders, it calls the internal WTP API directly (via reflection, to keep backward compat. https://github.com/sonatype/m2eclipse-wtp/commit/96acdcafaa233ebf00d3eb8dac00fe7f0d21d616#L5R562)
You can find more info about the upstream change in https://bugs.eclipse.org/bugs/show_bug.cgi?id=121460 and its attached patch : https://bugs.eclipse.org/bugs/attachment.cgi?id=201282&action=diff