There is no in-built override system for files in the includes/functions folder, but I recentyly figured out a method to do it by utilizing the override capabilities within the autoload/init_includes system.
First, make a copy of includes/init_includes/init_general_functions.php and save it in the includes/init_includes/overrides/ folder. Then edit that file to modify the loading of the html_output.php file so that it calls the file from an overrides folder like:
Then you can create your new folder includes/functions/overrides/, and put an edited copy of html_output in there. This way you can edit or add functions within html_output.php and not have to worry about duplicate functions warnings, or about your changes getting overwritten during an upgrade.
require(DIR_WS_FUNCTIONS . 'overrides/html_output.php');
You can use a similar method for overriding anything in the functions or classes folders, which don't have an inherent override capability.