magento 2: 'i18n:collect-phrases' command creates different csv files

The CSV with 4 columns is the global CSV for all modules. That's why it contains 3rd column as module and 4th column as Module_Name.This file should be placed in i18n folder parallel to app.

The CSV with 2 columns is the CSV required for each module. That's why module name is not specified in it. This file is located under i18n folder of each module.

The csv with 4 columns is used to create language package with composer.

In official doc http://devdocs.magento.com/guides/v2.1/config-guide/cli/config-cli-subcommands-i18n.html#config-cli-subcommands-xlate-dict :

-m | --magento Required to create a language package from this translation dictionary. If used, searches the directories that contain bin/magento. This option adds themes or modules to each line in the dictionary.