doc: fix mode and flags being mistaken in fs

Multiple `fs` functions have a `mode` and or `flag` option. In some
cases those have been mistaken and named wrongly. All of those faulty
entries have been fixed.
Besides that some indentation is also aligned with the rest of the
document.

PR-URL: https://github.com/nodejs/node/pull/27044


Reviewed-By: Ben Noordhuis <info@bnoordhuis.nl>
Reviewed-By: Rich Trott <rtrott@gmail.com>
Reviewed-By: Michaël Zasso <targos@protonmail.com>
Reviewed-By: James M Snell <jasnell@gmail.com>
Reviewed-By: Matteo Collina <matteo.collina@gmail.com>