Sorry for the delay on my reply to your request Michael. It's holiday time here so less resources, same amount of work
I did some reading about homeloader.so and it seems that this module is only added in the php.ini config in WHM when the "PHP Extensions and Applications Package" (found under Software -> Module Installers) is installed. Since this isn't done automatically during WHM install I assume a lot of users who didn't do this won't have an issue with homeloader.so and PHP5.4.
Sorry, I've no time at the moment to submit bug reports and especially no time to assist on one of our servers. What I can do is inform you this happened on all our servers. They all have "PHP Extensions and Applications Package" enabled. They all have homeloader.so in the PHP.ini config, which has not been added manually. One of the servers is a test server which is installed recently, just two weeks before this PHP upgrade, and is running basic WHM setup.
I am sure that if you have a fresh install on a CentOS 6.4 (minimal) and configure it with PHP 5.3 and "PHP Extensions and Applications Package" enabled, which will add homeloader.so to you PHP ini config, you can reproduce it by upgrading to PHP 5.4.