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'…).