setMetaData() should only be used to store customized data that describes something about the phar archive as a complete entity. PharFileInfo->setMetaData() should be used for file-specific meta-data. Meta-data can significantly slow down the performance of loading a phar archive if the data is large. As with all functionality that modifies the contents of a phar, the phar.readonly INI variable must be off in order to succeed.
Some possible uses for meta-data include specifying which file within the archive should be used to bootstrap the archive, or the location of a file manifest like PEAR's package.xml file. However, any useful data that describes the phar archive may be stored.