bootstrap: split NodeMainInstance::Run()

Split the running of the instance so that it can be reused
by the snapshot builder when we need to run the loop for
user code.

PR-URL: https://github.com/nodejs/node/pull/39007
Refs: https://github.com/nodejs/node/issues/35711
Refs: https://github.com/nodejs/node/pull/38905


Reviewed-By: James M Snell <jasnell@gmail.com>
Reviewed-By: Colin Ihrig <cjihrig@gmail.com>