You're right, everything in includes/modules/pages is not overrideable (is that a real word?
) at this time. The best bet is to create a backup copy of the original file (e.g. name it "header.php.bak") for safe keeping. Then, clearly comment everywhere that you make changes in the file.
Here's a real-world example from my own website. This is from the header file for checkout_success. I needed some extra checks certain products:
Code:
// START Modified 5/10/2006
// Frank Koehl
// Membership processing needs to see this data on each order
//if ($flag_global_notifications != '1') {
if (true) {
...
} // END if (true)
// END Modified 5/10/2006
This way, whenever I compare files for updates, the changes appear along with a clear explanation about what I did.