The Autotools plug-in autoconf editor allows setting of the macro versions to use for completion/hover in the Preferences dialog. This needs to be a Project property since projects will be at varying autoconf/automake levels.
Change has been made. A new Autotools page exists in the Project->Properties which has an Editors tab at present. This allows setting of the autoconf/automake macro versions to use for parsing for that project. The defaults are the defaults set up in the Preferences. If a file does not belong to the project, it will use the Preferences default, otherwise, it will use the settings here.