src: refactor bookkeeping of bootstrap status

This patch

1. Refactors the bootstrap routine of the main instance so that
  when --no-node-snapshot is used,
  Environment::InitializeMainContext() will only be called once
  (previously it would be called twice, which was harmless for now
  but not ideal).
2. Mark the number of BaseObjects in RunBootstrapping() when creating
  the Environment from scratch and in InitializeMainContext() when
  the Environment is deserialized. Previously the marking was done in
  the Environment constructor and InitializeMainContext() respectively
  for the cctest which was incorrect because the cctest never uses
  an Environment that's not bootstrapped. Also renames the mark
  to base_object_created_after_bootstrap to reflect what it's
  intended for.

PR-URL: https://github.com/nodejs/node/pull/37113
Refs: https://github.com/nodejs/node/pull/36943


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