src: run RunBeforeExitCallbacks as part of EmitBeforeExit

This is part of a series of changes to make embedding easier, by
requiring fewer internal methods to build a fully functioning
Node.js instance.

This also aligns the worker_threads code with the main thread code.

PR-URL: https://github.com/nodejs/node/pull/30229


Reviewed-By: Colin Ihrig <cjihrig@gmail.com>
Reviewed-By: Gireesh Punathil <gpunathi@in.ibm.com>
Reviewed-By: Joyee Cheung <joyeec9h3@gmail.com>
Reviewed-By: Shelley Vohr <codebytere@gmail.com>