As reported:

Contrary to the documentation, $wgRateLimits entry for 'user' overrides that for 'newbie'.

For example, with the following configuration, newly registered accounts are able to edit 10 pages per hour instead of 5:

$wgRateLimits[ 'edit' ] = [
  'user' => [ 10, 60*60 ],
  'newbie' => [ 5, 60*60 ],
];

This seems to be the opposite of what documentation in DefaultSettings.php says:

'newbie' => [ x, y ], // each new autoconfirmed accounts; overrides 'user'

(although that should probably be 'non-autoconfirmed'…).

Upstream bug:

https://phabricator.wikimedia.org/T169545

References:

https://lists.wikimedia.org/pipermail/mediawiki-announce/2018-September/000223.html