setVerticalMargin() adjusts also the vertical size available for the footer/header, see the attached files
footer-0.5in.pdf
$client->setVerticalMargin(".5in");
$client->setFooterHtml('<div style="background-color:#eee;height:36pt">footer</div>');
footer-1in.pdf
$client->setVerticalMargin("1in");
$client->setFooterHtml('<div style="background-color:#eee;height:72pt">footer</div>');