I have precisely the same setup. I have the add-on domain set to directory - let's call it /test - and inside test I have /wiki, which contains MediaWiki. /test is treated like public_html so put a .htaccess file there.
I have an .htaccess file there to point to the wiki using a Redirect.
Redirect /index.html http://www.trunker.org/wiki/
Should it be something else?
Works for me (set the rewrite rules & $wgScoiptPath correctly)
$wgScriptPath is set to "wiki/"
$wgScriptPath = "/wiki";
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