I've created a simple test application. It seems that I cannot attach files to closed issues, and now that I've created the test and reduced the scope, I'm unsure if this issue is the right one to attach the test to.
The problem was caused by the combination of jetty:run, Freemarker TLD loading and web overlays. When I remove the overlay, the TLD is loaded correctly, while the loading fails when the overlay exists in the POM. It also seems that it doesn't really matter what WAR I overlay the application, as the TLD lookup will fail no matter which one I add.