My plugin picks up each textdomain. Let’s assume, that you are using ‘woocommerce‘ and ‘woocommerce-admin‘. You will find both inside the drop down list of contained textdomains and will also face the warning for more than one textdomains.
By selecting one of them, you will only see those strings, that are related to the given textdomain. All the strings will be hosted within one *.po file. But if you generate the *.mo file, it depends on what textdomain is currently selected.
Generating the file for textdomain ‘woocommerce‘ will result in writing a file like: woocommerce-de_DE.mo
Generating the file for textdomain ‘woocommerce-admin‘ will result in writing a file like: woocommerce-admin-de_DE.mo
Both files only contains those strings related to the textdomain.
If your plugin loads both textdomains, than you will get all translations where needed. So the admin one should be loaded only, if you are logged in and working within admin pages.
Hint: My plugin uses the first found textdomain as the main one. The order of load call appearance in PHP code will determine the choise of plugins main textdomain.