We are also having EZProxy setting wrong URL for the iframe; and instead of fixing the absolute URL, we decided to use relative URI instead:
$relativeUrl = '/index.php/' . $journal->getPath() . '/article/download/' . $article->getBestArticleId() . '/' . $galley->getBestGalleyId()
This variable is calculated within the plugin class, and replaces the $pdfUrl in the iframe src attribute.
Would this cause any issues? @ctgraham or someone else who knows.
Sean