Hmmm… yes, HTMLPurifier’s defaults will still prevent ids and script tags even if the allowed_html is modified.
This will require a code modification to the PKPString::stripUnsafeHtml() function in lib/pkp/classes/core/PKPString.inc.php:
The configuration options are documented here:
http://htmlpurifier.org/live/configdoc/plain.html
You’re probably interested in “EnableID” and “SafeScripting”.