What do you mean by "javascript popup confirm box"?

Is it the kind of dialog box like the one opened by a call to the Javascript/browser alert() function or is it some HTML that asks for confirmation?

If it is a call to alert(), then the easiest approach is to replace that confirmation button with a Javascript function that returns the result you want:

$mech->evaluate_in_page(<<'JS');
    window.alert = function(msg) { return true };
JS
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