src,fs: calculate fs times without truncation

also added some missing bits that didn't make it into #12818

PR-URL: https://github.com/nodejs/node/pull/12607
Refs: https://github.com/nodejs/node/pull/12818


Reviewed-By: Timothy Gu <timothygu99@gmail.com>
Reviewed-By: Refael Ackermann <refack@gmail.com>
Reviewed-By: Anna Henningsen <anna@addaleax.net>
Reviewed-By: James M Snell <jasnell@gmail.com>