Most, if not all functional test modules have XAR dependencies and those are installed as extensions inside XWiki. Thus at XWiki initialization time, the Extension Manager initializes those extensions and need to have the JAR Extension Handler available to do so.
According to Thomas the reason it wasn't failing before is:
ok I know why actually, the code of package mojo did not changed (still using the old packager plugin) but now an extension repository is automatically registered based on the running Maven session so now it find the extensions it's importing and register it
so they were not registered as extension before (so installed extension when starting XWiki)