Please just use |{{int:preferences}}]] instead of
$ cd messages; perl -nlwe 'for(/\Q[[Special:Preferences\E.*\]/g){print}' MessagesEn.php
[[Special:Preferences|{{SITENAME}} preferences]]
[[Special:Preferences|account preferences]]
[[Special:Preferences|user preferences]]
[[Special:Preferences|user preferences]]
[[Special:Preferences|preferences]]
[[Special:Preferences|your user preferences]]
[[Special:Preferences|user preferences]]
Same for other languages too. Speaking of which,
$ perl -nlwe "if(/'welcome/../',$/)"'{$h{$ARGV}.=$_}END{for(keys %h){$q++ if $h{$_}!~/SITENAME/}print $q}' *
36
of them mention {{SITENAME}} in the welcome string. Perhaps don't.
$ perl -nlwe "if(/'welcome/../',$/)"'{$h{$ARGV}.=$_}END{for(keys %h){$q++ if $h{$_}!~/Preferences/}print $q}' *
94
of them give a link. The rest should too.

OK, let's have a look at a few:
$ perl -nlwe "if(/'welcome/../',$/){print}" *Zh*
'welcomecreation' => '== 欢迎, $1! ==

您的账户已经建立，不要忘记设置[[Special:Preferences|{{SITENAME}}的个人参数]]。',

'welcomecreation' => '<h2>歡迎，$1!</h2><p>您的帳號已經建立，不要忘記設置[[Special:Preferences|{{SITENAME}}個人參數]]。</p>',
'welcomecreation' => '<h2>歡迎，$1!</h2><p>您的帳號已經建立，不要忘記設置{{SITENAME}}個人參數。</p>',
We observe wide variation.

Version: 1.16.x
Severity: enhancement