Not sure if my problem is related to your exact problem, but it’s related to wp-blog-header.php being broken. From the release of 5.4.1, I had many tickets from clients complaining their WP websites are not working. What I could confirm was that the wp-blog-header.php file was empty (0 bytes) on all of those installations and restoring that file from the official WP package (or a backup) solved the problem. Last one was today. I’m not sure about the old tickets because I haven’t checked at that time, but the one I got today, WP was installed using Softaculous, so, I’m not sure if the problem was a WP updater problem, or more possible a Softaculous problem.