esm: remove CLI flag limitation to programmatic registration

[JakobJingleheimer]

This is a follow-up to #46826

We see 2 potential approaches here when we detect a user is trying to register a loader and the worker etc have not be set up:

1. Replace the existing DefaultModuleLoader with a CustomizedModuleLoader
2. Merge the two ModuleLoaders back together and trigger setups when certain methods are called (eg ModuleLoader::register())

The first seems the simplest. However, it's currently facing an issue where ModuleJob maintains a reference to the loader that instantiated it; in option 1, that reference becomes stale. Further work to be done is to sever their direct connection.