The countries configurator is a simple module thate make it possible to change the order of the countries list and which countries are shown.
In the system settings, you can configure the system wide available countries. In a root page, you can configure the available countries for a page tree.
Currently the getCountries hook does not support modifications on the countries list (remove countries). I make'd a pull request to solve this problem, I hope the request will be added shortly. contao/core#4331