First I take a copy of the header.php before I made changes.
After I made changes to the header like the default image and header text through the dashboard
I reopened the header.php and find no changes there.
My assumption is when changes being made through Dashboard then dynamically the corresponding php files would updated. No?
If not, how would be changes in Dashboard be reflected in php file?
If you’re making your changes to the header.php files via Appearances >> Editor >> Header.php … then of course you’re altering your header.php file.
You can also accomplish this by FTPing the file or using your server’s control panel.
But before you make all these changes to your core WordPress files, I’d have to ask — “why”? It’s never (recommended) to make changes to your core WordPress files. This is because when you go to update your WordPress the next time an update comes out, you’ll lose all your changes … so you’ll have to keep a changelog of your edits or end up with a dinosaur version of WP in the future.
If your theme doesn’t give you an opportunity to do so alter the header in other manners, perhaps a plugin is a better solution. Or perhaps using custom CSS is a better solution if that fits your need. What are you trying to accomplish? Why would it need a moderation of a WP core file? Most likely, there are other ways to accomplish your goal(s).