This is because $wgAddPersonalUrlsTable
does not replace the settings in extension.json
but is merged into them. This is the normal way configuration works now in MediaWiki. I just corrected the extension documentation which was outdated in this regard.
Thanks for attracting my attention to the fact that this requires a mechanism to deactivate predefined items. To solve this, I have just created version 1.2.1 (and merged it into the branches for MW 1.30, 1.31 and 1.32). With this, you can override as follows:
wfLoadExtension( 'AddPersonalUrls' );
$wgAddPersonalUrlsTable = array(
'addpersonalurls-home' => NULL,
'addpersonalurls-userpages' => 'Special:PrefixIndex?prefix=$username&namespace=2',
'addpersonalurls-favorites' => 'Special:Mypage/Favoriten',
'addpersonalurls-sandbox' => 'Special:Mypage/Spielwiese',
'addpersonalurls-notes' => 'Special:Mypage/Notizen'
);