The single link tool adds normal hyperlinks, not redirect links.
For instance, if you add a link from your post example.com/newpost to an older post like example.com/olderpost, the link will be the same as if you hand-coded it.
e.g. <a href="http://example.com/olderpost">cool older story</a>
So, if for some reason you ever did uninstall Contextly, the links in the body of your posts will still work.