lib: move setupAllowedFlags() into per_thread.js

Because most of its code (the getter) has nothing to do with
the actual bootstrapping and it is run per-thread.

PR-URL: https://github.com/nodejs/node/pull/24704


Reviewed-By: Anna Henningsen <anna@addaleax.net>
Reviewed-By: Christopher Hiller <boneskull@boneskull.com>