The DatabaseInitializer is called during first boot
(`CRM_Core_Config::singleton()`) and runs `system.flush session=1
triggers=1` which (among other things) enumerates modules (including CMS
modules).  In standalone boot protocol, that means it runs before
`CRM_Utils_System::loadBootstrap()` (which means that CMS modules
cannot be enumerated yet).

A simple work-around is to always boot the CMS first (before
`CRM_Core_Config::singleton()` or `DatabaseInitializer` runs).