OK, I get what your saying Site Improve still throws errors (which sucks since the search is on every page of the site and my agency uses it to help asses things).
I have found though that the aria-hidden can be added to the new fieldset and legend. I went ahead and implemented this change with jQuery, which at least will resolve it for my site without having to edit the plugin itself.
Example output:
<fieldset aria-hidden=”true” id=”hiddenset” style=””>
<legend aria-hidden=”true” style=”transition: none 0s ease 0s;”>Custom Set</legend>
<input type=”checkbox” style=”display: none !important;” value=”page” aria-label=”Hidden label” aria-hidden=”true” id=”2_1customset_2_1100″ name=”customset[]” checked=”checked”>
<input type=”checkbox” style=”display: none !important;” value=”tribe_events” aria-label=”Hidden label” aria-hidden=”true” id=”2_1customset_2_1101″ name=”customset[]” checked=”checked”>
</fieldset>