The Apache HTTP Server can be configured in a number of ways: The main configuration file is (usually) called "httpd.conf", but this file can include other configuration files with the "Include" directive. Furthermore, the HTTP Server allows for configuration files to be placed in the context path of your website. These decentral configuration files are (usually) called ".htaccess".
Configuration directives, like the directives to enable compression, can be valid in different contexts. The valid configuration contexts of the "AddOutputFilter", the "SetOutputFilter", and the (deprecated) "AddOutputFilterByType" all specify "server config, virtual host, directory, .htaccess" as their valid configuration contexts. Therefore, all of these directives can be used in the "httpd.conf" as well as in the ".htaccess" configuration files.
So both ways of configuring output compression are valid, and it's just a matter of taste whether you want all your server configuration in one central file (which gets only read during server (re)start) or whether want to spread the configuration in multiple files and directories (but get the benefit of changes being applied instantly).