I have this code that opens the file and replaces a string using replaceText.
var url = \'http://www.test.com\';
var doc = DocumentApp.openById(file.getId())
Here is how it goes, at least if you have only one occurrence of the url placeHolder.
If you have more than one then you should iterate the whole doc content to find each or them and replace them all.
function myFunction() {
var url = 'http://www.google.com';
var doc = DocumentApp.getActiveDocument();// or DocumentApp.openById(file.getId()); as in your example code
var element = doc.getBody().findText("<<urlGoesHere>>");
if(element){ // if found a match
var start = element.getStartOffset();
var text = element.getElement().asText();
text.replaceText("<<urlGoesHere>>",url);
text.setLinkUrl(start, start+url.length, url);
doc.saveAndClose();
} // else do nothing
}