This is a "feature" of the M2E plugin that had been introduced a while ago. It's not directly related to the JBoss EAR plugin but also happens with most other Maven plugins.
If you have a plugin execution defined in your pom (like the execution of maven-ear-plugin:generate-application-xml), you also need to add additional config information for M2E that tells M2E what to do when the build is run in Eclipse, e.g. should the plugin execution be ignored or executed by M2E, should it be also done for incremental builds, ... If that information is missing, M2E complains about it by showing the "Plugin execution not covered by lifecycle configuration" error message.
See here for a more detailed explanation and some sample config that needs to be added to the pom to make that error go away: