When I wrote my first special page this manual page confused me a lot. It seemed to me that it was saying to use my i18n file and put my $specialPageAliases and that the .alias.php file was deprecated. From discussions from people involved with translatewiki.net, this is not the case. You still need to put $specialPageAliases into a .alias.php file seperate from your $messages .i18n.php file, (even though core put thems together), just load both using $wgExtensionMessagesFiles[] instead of one with $wgExtensionMessagesFiles and the other $wgExtensionAliasesFiles. The manual page should really be changed to make this clearer, but since I'm not 100% certain I have all my facts straight (and since there are no facts documented out there) I'll put it here for now.