The Node System Links module (nodesyslinks) provides an input filter which converts internal node links from their aliased path to their system path.
In an ideal world the formatter would look to see if there is an internal aliased node link and will convert it to /node/99.
Let's say you have an Article content type with a body field, and the body field contains links which have been added via the WYSIWYG editor. The links will pretty much always have been added to point to an aliased path, e.g. website.com/about-us rather than a system path such as website.com/node/99.